21-38693982-T-G

Variant names:

• chr21-38693982-T-G
• rs2836631

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 0.465 in 152,048 control chromosomes in the GnomAD database, including 16,886 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 0.47 (16886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70639 AN: 151928 Hom.: 16858 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.465 AC: 70715 AN: 152048 Hom.: 16886 Cov.: 32 AF XY: 0.458 AC XY: 34017 AN XY: 74322

African (AFR) AF: 0.511 AC: 21176 AN: 41444

American (AMR) AF: 0.367 AC: 5603 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2064 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5164

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4167 AN: 10584

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32754 AN: 67974

Other (OTH) AF: 0.494 AC: 1045 AN: 2114

Alfa AF: 0.453 Hom.: 3343

Bravo AF: 0.466

Asia WGS AF: 0.330 AC: 1145 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	1.8
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2836631; hg19: chr21-40065906;