Genetic Variant NM_001143998.2:c.*1103C>T (chr17-77215126-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001143998.2(SEC14L1):c.*1103C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 984,906 control chromosomes in the GnomAD database, including 417 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.023 ( 62 hom., cov: 32)

Exomes 𝑓: 0.029 ( 355 hom. )

Consequence

SEC14L1
NM_001143998.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.61

Publications

13 publications found

Variant links:

Genes affected

SEC14L1 (HGNC:10698): (SEC14 like lipid binding 1) The protein encoded by this gene belongs to the SEC14 cytosolic factor family. It has similarity to yeast SEC14 and to Japanese flying squid RALBP which suggests a possible role of the gene product in an intracellular transport system. Multiple alternatively spliced transcript variants have been found for this gene; some variants represent read-through transcripts that include exons from the upstream gene C17orf86. [provided by RefSeq, Feb 2011]

SEC14L1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC14L1	NM_001143998.2 link	c.*1103C>T		3_prime_UTR_variant	Exon 17 of 17	ENST00000436233.9	NP_001137470.2	Q92503-1A0A024R8V1Q7Z3R7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SEC14L1	ENST00000436233.9 link	c.*1103C>T	3_prime_UTR_variant	Exon 17 of 17	1	NM_001143998.2	ENSP00000390392.3	Q92503-1
SEC14L1	ENST00000443798.8 link	c.2144+1107C>T	intron_variant	Intron 17 of 17	1		ENSP00000406030.3	Q92503-2
SEC14L1	ENST00000430767.8 link	c.*1103C>T	3_prime_UTR_variant	Exon 18 of 18	2		ENSP00000408169.3	Q92503-1
SEC14L1	ENST00000392476.6 link	c.2144+1107C>T	intron_variant	Intron 19 of 19	2		ENSP00000376268.2	Q92503-2

Frequencies

GnomAD3 genomes

AF:

0.0232

AC:

3507

AN:

151482

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00578

Gnomad AMI

AF:

0.165

Gnomad AMR

AF:

0.0252

Gnomad ASJ

AF:

0.0445

Gnomad EAS

AF:

0.00522

Gnomad SAS

AF:

0.0598

Gnomad FIN

AF:

0.0234

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.0287

Gnomad OTH

AF:

0.0284

GnomAD4 exome

AF:

0.0289

AC:

24046

AN:

833306

Hom.:

355

Cov.:

AF XY:

0.0289

AC XY:

11103

AN XY:

384844

show subpopulations

African (AFR)

AF:

0.00500

AC:

AN:

15790

American (AMR)

AF:

0.0183

AC:

AN:

986

Ashkenazi Jewish (ASJ)

AF:

0.0365

AC:

188

AN:

5152

East Asian (EAS)

AF:

0.00468

AC:

AN:

3630

South Asian (SAS)

AF:

0.0664

AC:

1098

AN:

16524

European-Finnish (FIN)

AF:

0.0199

AC:

AN:

302

Middle Eastern (MID)

AF:

0.0351

AC:

AN:

1626

European-Non Finnish (NFE)

AF:

0.0286

AC:

21781

AN:

761986

Other (OTH)

AF:

0.0294

AC:

802

AN:

27310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

1327

2655

3982

5310

6637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1160

2320

3480

4640

5800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0231

AC:

3500

AN:

151600

Hom.:

Cov.:

AF XY:

0.0239

AC XY:

1766

AN XY:

74030

show subpopulations

African (AFR)

AF:

0.00576

AC:

238

AN:

41296

American (AMR)

AF:

0.0252

AC:

383

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.0445

AC:

154

AN:

3462

East Asian (EAS)

AF:

0.00524

AC:

AN:

5156

South Asian (SAS)

AF:

0.0591

AC:

283

AN:

4792

European-Finnish (FIN)

AF:

0.0234

AC:

245

AN:

10484

Middle Eastern (MID)

AF:

0.0479

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0287

AC:

1948

AN:

67890

Other (OTH)

AF:

0.0277

AC:

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

173

347

520

694

867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0266

Hom.:

132

Bravo

AF:

0.0215

Asia WGS

AF:

0.0320

AC:

110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.13

(source)

DANN

Benign

0.75

PhyloP100

-3.6

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

3.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over