rs16856186

Variant names:

• chr1-205708998-T-G
• rs16856186

Variant summary

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

The variant allele was found at a frequency of 0.0526 in 152,258 control chromosomes in the GnomAD database, including 282 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 0.053 (282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0681 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 8016 AN: 152140 Hom.: 282 Cov.: 31

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0526 AC: 8013 AN: 152258 Hom.: 282 Cov.: 31 AF XY: 0.0522 AC XY: 3886 AN XY: 74454

African (AFR) AF: 0.0358 AC: 1488 AN: 41538

American (AMR) AF: 0.0318 AC: 486 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3466

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5186

South Asian (SAS) AF: 0.0526 AC: 254 AN: 4828

European-Finnish (FIN) AF: 0.0736 AC: 780 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0698 AC: 4745 AN: 68020

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0620 Hom.: 956

Bravo AF: 0.0493

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs16856186; hg19: chr1-205678126; COSMIC: COSV65652643;