16-2203772-A-G

Variant names:

• chr16-2203772-A-G
• rs26865

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 0.416 in 152,074 control chromosomes in the GnomAD database, including 15,899 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 0.42 (15899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.416 AC: 63265 AN: 151956 Hom.: 15902 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 63278 AN: 152074 Hom.: 15899 Cov.: 32 AF XY: 0.422 AC XY: 31382 AN XY: 74342

African (AFR) AF: 0.118 AC: 4894 AN: 41538

American (AMR) AF: 0.495 AC: 7563 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3032 AN: 5180

South Asian (SAS) AF: 0.526 AC: 2532 AN: 4816

European-Finnish (FIN) AF: 0.571 AC: 6035 AN: 10562

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36450 AN: 67930

Other (OTH) AF: 0.417 AC: 878 AN: 2108

Alfa AF: 0.483 Hom.: 27408

Bravo AF: 0.394

Asia WGS AF: 0.521 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs26865; hg19: chr16-2253773;