rs915854

Variant names:

• chr21-43046656-C-T
• rs915854

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.62 (30352 hom., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 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: 0.620 AC: 81027 AN: 130636 Hom.: 30329 Cov.: 20

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.620 AC: 81098 AN: 130754 Hom.: 30352 Cov.: 20 AF XY: 0.621 AC XY: 39085 AN XY: 62982

African (AFR) AF: 0.619 AC: 22954 AN: 37076

American (AMR) AF: 0.608 AC: 8183 AN: 13456

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1666 AN: 3188

East Asian (EAS) AF: 0.719 AC: 3449 AN: 4798

South Asian (SAS) AF: 0.622 AC: 2416 AN: 3882

European-Finnish (FIN) AF: 0.628 AC: 4744 AN: 7560

Middle Eastern (MID) AF: 0.523 AC: 138 AN: 264

European-Non Finnish (NFE) AF: 0.622 AC: 36020 AN: 57904

Other (OTH) AF: 0.598 AC: 1117 AN: 1868

Alfa AF: 0.568 Hom.: 3188

Asia WGS AF: 0.534 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.38
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs915854; hg19: chr21-44466766; COSMIC: COSV53455533;