rs16856874

Variant names:

• chr1-232358378-G-A
• rs16856874

Your query was ambiguous. Multiple possible variants found:

• chr1-232358378-G-A
• chr1-232358378-G-T

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 0.0737 in 152,148 control chromosomes in the GnomAD database, including 518 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 0.074 (518 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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: 0.0737 AC: 11209 AN: 152030 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0737 AC: 11212 AN: 152148 Hom.: 518 Cov.: 32 AF XY: 0.0755 AC XY: 5612 AN XY: 74366

African (AFR) AF: 0.0429 AC: 1782 AN: 41522

American (AMR) AF: 0.111 AC: 1698 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.169 AC: 873 AN: 5166

South Asian (SAS) AF: 0.0797 AC: 384 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1087 AN: 10576

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4804 AN: 67996

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0692 Hom.: 662

Bravo AF: 0.0760

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs16856874; hg19: chr1-232494124;