chr21-38662796-A-T

Variant names:

• chr21-38662796-A-T
• rs8132203

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 0.969 in 152,342 control chromosomes in the GnomAD database, including 71,628 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 0.97 (71628 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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: 0.969 AC: 147563 AN: 152224 Hom.: 71560 Cov.: 31

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.969 AC: 147690 AN: 152342 Hom.: 71628 Cov.: 31 AF XY: 0.970 AC XY: 72285 AN XY: 74490

African (AFR) AF: 0.991 AC: 41198 AN: 41576

American (AMR) AF: 0.969 AC: 14827 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3428 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5184

South Asian (SAS) AF: 0.989 AC: 4775 AN: 4828

European-Finnish (FIN) AF: 0.972 AC: 10330 AN: 10624

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64761 AN: 68034

Other (OTH) AF: 0.962 AC: 2031 AN: 2112

Alfa AF: 0.964 Hom.: 8880

Bravo AF: 0.969

Asia WGS AF: 0.995 AC: 3462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.067
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs8132203; hg19: chr21-40034720;