chr21-38693982-T-G

Variant names:

• chr21-38693982-T-G
• rs2836631

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 0.465 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.465 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

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.494

Alfa AF: 0.452 Hom.: 3253

Bravo AF: 0.466

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836631; hg19: chr21-40065906;