rs16917302

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285837	ENST00000647733.1	c.981+41642A>C		intron_variant	Intron 4 of 7			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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0986

Gnomad4 OTH AF: 0.162

Alfa AF: 0.113 Hom.: 1928

Bravo AF: 0.184

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16917302; hg19: chr10-64261198;