chr21-46155876-A-C

Variant names:

• chr21-46155876-A-C
• rs914246

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 0.613 in 152,250 control chromosomes in the GnomAD database, including 29,396 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 0.61 (29396 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.613 AC: 93278 AN: 152132 Hom.: 29383 Cov.: 36

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.613 AC: 93317 AN: 152250 Hom.: 29396 Cov.: 36 AF XY: 0.601 AC XY: 44734 AN XY: 74438

African (AFR) AF: 0.684 AC: 28408 AN: 41556

American (AMR) AF: 0.489 AC: 7483 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1354 AN: 5168

South Asian (SAS) AF: 0.506 AC: 2441 AN: 4828

European-Finnish (FIN) AF: 0.549 AC: 5823 AN: 10602

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43283 AN: 68000

Other (OTH) AF: 0.611 AC: 1292 AN: 2114

Alfa AF: 0.637 Hom.: 4828

Bravo AF: 0.612

Asia WGS AF: 0.402 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		-0.42
PromoterAI		-0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs914246; hg19: chr21-47575790; COSMIC: COSV52429329;