rs395640

Variant names:

• chr21-26597540-A-G
• rs395640

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;