Genetic Variant ENST00000619483.4:n.2540T>C (chr22-30423640-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000619483.4(SEC14L2):n.2540T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,386 control chromosomes in the GnomAD database, including 7,770 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 0.32 ( 7758 hom., cov: 34)

Exomes 𝑓: 0.33 ( 12 hom. )

Consequence

SEC14L2
ENST00000619483.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

17 publications found

Variant links:

Genes affected

SEC14L2 (HGNC:10699): (SEC14 like lipid binding 2) This gene encodes a cytosolic protein which belongs to a family of lipid-binding proteins including Sec14p, alpha-tocopherol transfer protein, and cellular retinol-binding protein. The encoded protein stimulates squalene monooxygenase which is a downstream enzyme in the cholesterol biosynthetic pathway. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]

SEC14L2 links:

ENSG00000249590 (HGNC:):

ENSG00000249590 links:

Genome browser will be placed here

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SEC14L2	NM_012429.5 link	c.*1233T>C	3_prime_UTR_variant	Exon 12 of 12	ENST00000615189.5	NP_036561.1	O76054-1A0A024R1I5
SEC14L2	NM_001291932.2 link	c.*1233T>C	3_prime_UTR_variant	Exon 11 of 11		NP_001278861.1	B7Z3Z8
SEC14L2	NM_001204204.3 link	c.*1233T>C	3_prime_UTR_variant	Exon 10 of 10		NP_001191133.1	O76054-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC14L2	ENST00000615189.5 link	c.*1233T>C		3_prime_UTR_variant	Exon 12 of 12	1	NM_012429.5	ENSP00000478755.1		O76054-1
ENSG00000249590	ENST00000439838.5 link	c.584-3077T>C		intron_variant	Intron 6 of 8	2		ENSP00000415178.1		H7C417

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48172

AN:

152102

Hom.:

7753

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.331

AC:

AN:

166

Hom.:

Cov.:

AF XY:

0.343

AC XY:

AN XY:

134

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.313

AC:

AN:

150

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.317

AC:

48213

AN:

152220

Hom.:

7758

Cov.:

AF XY:

0.321

AC XY:

23911

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.327

AC:

13601

AN:

41544

American (AMR)

AF:

0.338

AC:

5177

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

805

AN:

3470

East Asian (EAS)

AF:

0.376

AC:

1945

AN:

5172

South Asian (SAS)

AF:

0.353

AC:

1706

AN:

4832

European-Finnish (FIN)

AF:

0.343

AC:

3639

AN:

10600

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20197

AN:

67980

Other (OTH)

AF:

0.315

AC:

667

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1785

3570

5356

7141

8926

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.297

Hom.:

9414

Bravo

AF:

0.313

Asia WGS

AF:

0.398

AC:

1379

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.3

(source)

DANN

Benign

0.73

PhyloP100

-1.1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

ENST00000619483.4:n.2540T>C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over