17-77215126-C-T

Variant names:

• chr17-77215126-C-T
• rs3744064
• NM_001143998.2:c.*1103C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61
• Publications: 13 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143998.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC14L1	NM_001143998.2	MANE Select	c.*1103C>T		3_prime_UTR	Exon 17 of 17	NP_001137470.2
	SEC14L1	NM_001143999.2		c.*1103C>T		3_prime_UTR	Exon 17 of 17	NP_001137471.2
	SEC14L1	NM_001204410.2		c.*1103C>T		3_prime_UTR	Exon 19 of 19	NP_001191339.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC14L1	ENST00000436233.9	TSL:1 MANE Select	c.*1103C>T		3_prime_UTR	Exon 17 of 17	ENSP00000390392.3
	SEC14L1	ENST00000443798.8	TSL:1	c.2144+1107C>T		intron	N/A	ENSP00000406030.3
	SEC14L1	ENST00000430767.8	TSL:2	c.*1103C>T		3_prime_UTR	Exon 18 of 18	ENSP00000408169.3

Frequencies

GnomAD3 genomes AF: 0.0232 AC: 3507 AN: 151482 Hom.: 63 Cov.: 32

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.: 31 AF XY: 0.0289 AC XY: 11103 AN XY: 384844

African (AFR) AF: 0.00500 AC: 79 AN: 15790

American (AMR) AF: 0.0183 AC: 18 AN: 986

Ashkenazi Jewish (ASJ) AF: 0.0365 AC: 188 AN: 5152

East Asian (EAS) AF: 0.00468 AC: 17 AN: 3630

South Asian (SAS) AF: 0.0664 AC: 1098 AN: 16524

European-Finnish (FIN) AF: 0.0199 AC: 6 AN: 302

Middle Eastern (MID) AF: 0.0351 AC: 57 AN: 1626

European-Non Finnish (NFE) AF: 0.0286 AC: 21781 AN: 761986

Other (OTH) AF: 0.0294 AC: 802 AN: 27310

GnomAD4 genome AF: 0.0231 AC: 3500 AN: 151600 Hom.: 62 Cov.: 32 AF XY: 0.0239 AC XY: 1766 AN XY: 74030

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: 27 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: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0287 AC: 1948 AN: 67890

Other (OTH) AF: 0.0277 AC: 58 AN: 2096

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.13
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)

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

Other links and lift over

dbSNP: rs3744064; hg19: chr17-75211208;