rs395640

chr21-26597540-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 0.792 in 152,132 control chromosomes in the GnomAD database, including 47,786 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 0.79 (47786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.792 AC: 120451 AN: 152014 Hom.: 47749 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.792 AC: 120547 AN: 152132 Hom.: 47786 Cov.: 32 AF XY: 0.792 AC XY: 58873 AN XY: 74344

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.809

Alfa AF: 0.793 Hom.: 62837

Bravo AF: 0.793

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.0040
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs395640; hg19: chr21-27969859;