rs3744064

Positions:

• chr17-77215126-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SEC14L1	NM_001143998.2	c.*1103C>T		3_prime_UTR_variant	17/17	ENST00000436233.9	NP_001137470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC14L1	ENST00000436233.9	c.*1103C>T		3_prime_UTR_variant	17/17	1	NM_001143998.2	ENSP00000390392
SEC14L1	ENST00000443798.8	c.2144+1107C>T		intron_variant		1		ENSP00000406030	P1
SEC14L1	ENST00000430767.8	c.*1103C>T		3_prime_UTR_variant	18/18	2		ENSP00000408169
SEC14L1	ENST00000392476.6	c.2144+1107C>T		intron_variant		2		ENSP00000376268	P1

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

Gnomad4 AFR exome AF: 0.00500

Gnomad4 AMR exome AF: 0.0183

Gnomad4 ASJ exome AF: 0.0365

Gnomad4 EAS exome AF: 0.00468

Gnomad4 SAS exome AF: 0.0664

Gnomad4 FIN exome AF: 0.0199

Gnomad4 NFE exome AF: 0.0286

Gnomad4 OTH exome AF: 0.0294

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

Gnomad4 AFR AF: 0.00576

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.00524

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.0287

Gnomad4 OTH AF: 0.0277

Alfa AF: 0.0283 Hom.: 94

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
DANN	Benign	0.75
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		3.2

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

LitVar

Other links and lift over

dbSNP: rs3744064; hg19: chr17-75211208;