rs16856186

Variant names:

• chr1-205708998-T-G
• rs16856186

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 0.0526 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0527 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

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0642 Hom.: 495

Bravo AF: 0.0493

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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