21-38693982-T-G

Position:

• chr21-38693982-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;