chr21-38964966-A-G

Position:

• chr21-38964966-A-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 0.718 in 150,252 control chromosomes in the GnomAD database, including 38,925 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 0.72 (38925 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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: 0.718 AC: 107816 AN: 150142 Hom.: 38898 Cov.: 26

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.718 AC: 107888 AN: 150252 Hom.: 38925 Cov.: 26 AF XY: 0.716 AC XY: 52423 AN XY: 73174

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.671

Alfa AF: 0.708 Hom.: 17693

Bravo AF: 0.710

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836788; hg19: chr21-40336891;