rs395640

Variant names:

• chr21-26597540-A-G
• rs395640

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.796 AC: 33071 AN: 41522

American (AMR) AF: 0.803 AC: 12274 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2764 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4153 AN: 5164

South Asian (SAS) AF: 0.748 AC: 3608 AN: 4824

European-Finnish (FIN) AF: 0.807 AC: 8540 AN: 10586

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53646 AN: 67970

Other (OTH) AF: 0.809 AC: 1710 AN: 2114

Alfa AF: 0.793 Hom.: 79984

Bravo AF: 0.793

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.23
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs395640; hg19: chr21-27969859;