rs16969682

Variant names:

• chr17-77130930-A-C
• rs16969682
• NM_001204408.2:c.-135-11716A>C

Variant summary

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

The NM_001204408.2(SEC14L1):​c.-135-11716A>C variant causes a intron 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: SEC14L1 NM_001204408.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 9 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]

LOC105371901 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204408.2. 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_001204408.2		c.-135-11716A>C		intron	N/A	NP_001191337.2
	SEC14L1	NM_001204410.2		c.-135-11716A>C		intron	N/A	NP_001191339.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC14L1	ENST00000392476.6	TSL:2	c.-135-11716A>C		intron	N/A	ENSP00000376268.2
	SEC14L1	ENST00000430767.8	TSL:2	c.-135-11716A>C		intron	N/A	ENSP00000408169.3
	SEC14L1	ENST00000589827.5	TSL:2	c.-135-11716A>C		intron	N/A	ENSP00000464973.1

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

African (AFR) AF: 0.0558 AC: 2317 AN: 41510

American (AMR) AF: 0.190 AC: 2902 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2117 AN: 5168

South Asian (SAS) AF: 0.115 AC: 557 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2237 AN: 10570

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10329 AN: 67972

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.152 Hom.: 6637

Bravo AF: 0.144

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		0.22
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: rs16969682; hg19: chr17-75127012;