rs16917302

Variant names:

• chr10-62501439-A-C
• rs16917302
• ENST00000647733.1:c.981+41642A>C

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.981+41642A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,050 control chromosomes in the GnomAD database, including 3,205 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 0.18 (3205 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 14 publications found

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647733.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285837	ENST00000647733.1		c.981+41642A>C		intron	N/A	ENSP00000502188.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26979 AN: 151932 Hom.: 3194 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.178 AC: 27023 AN: 152050 Hom.: 3205 Cov.: 32 AF XY: 0.178 AC XY: 13264 AN XY: 74318

African (AFR) AF: 0.339 AC: 14049 AN: 41420

American (AMR) AF: 0.140 AC: 2143 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.193 AC: 1000 AN: 5176

South Asian (SAS) AF: 0.103 AC: 495 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1684 AN: 10582

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0986 AC: 6706 AN: 68002

Other (OTH) AF: 0.162 AC: 341 AN: 2106

Alfa AF: 0.130 Hom.: 4939

Bravo AF: 0.184

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs16917302; hg19: chr10-64261198;