rs16969682

Positions:

• chr17-77130930-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_934988.3(LOC105371901):​n.311-5113T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,102 control chromosomes in the GnomAD database, including 1,944 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 0.14 (1944 hom., cov: 32)
• Consequence: LOC105371901 XR_934988.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

LOC105371901 (HGNC:):

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371901	XR_934988.3	n.311-5113T>G		intron_variant, non_coding_transcript_variant
SEC14L1	NM_001204408.2	c.-135-11716A>C		intron_variant			NP_001191337.2
SEC14L1	NM_001204410.2	c.-135-11716A>C		intron_variant			NP_001191339.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC14L1	ENST00000392476.6	c.-135-11716A>C		intron_variant		2		ENSP00000376268	P1
SEC14L1	ENST00000430767.8	c.-135-11716A>C		intron_variant		2		ENSP00000408169
SEC14L1	ENST00000561721.6	c.-135-11716A>C		intron_variant		2		ENSP00000466079

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21798 AN: 151984 Hom.: 1946 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21796 AN: 152102 Hom.: 1944 Cov.: 32 AF XY: 0.149 AC XY: 11106 AN XY: 74362

Gnomad4 AFR AF: 0.0558

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.146

Alfa AF: 0.156 Hom.: 4253

Bravo AF: 0.144

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.79

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: rs16969682; hg19: chr17-75127012;