rs16936517

Variant names:

• chr10-37444453-C-T
• rs16936517

Variant summary

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

The variant allele was found at a frequency of 0.103 in 152,136 control chromosomes in the GnomAD database, including 982 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 0.10 (982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15540 AN: 152018 Hom.: 954 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0749

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.103 AC: 15620 AN: 152136 Hom.: 982 Cov.: 32 AF XY: 0.102 AC XY: 7602 AN XY: 74368

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0799 Hom.: 597

Bravo AF: 0.107

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.091

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16936517; hg19: chr10-37733381;