chr21-41548095-G-A

Variant names:

• chr21-41548095-G-A
• rs1041834

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 0.56 in 151,942 control chromosomes in the GnomAD database, including 24,928 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 0.56 (24928 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 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: 0.561 AC: 85113 AN: 151820 Hom.: 24928 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.560 AC: 85137 AN: 151942 Hom.: 24928 Cov.: 31 AF XY: 0.554 AC XY: 41107 AN XY: 74266

African (AFR) AF: 0.406 AC: 16807 AN: 41438

American (AMR) AF: 0.579 AC: 8839 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2558 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2177 AN: 5166

South Asian (SAS) AF: 0.542 AC: 2603 AN: 4802

European-Finnish (FIN) AF: 0.521 AC: 5501 AN: 10550

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44693 AN: 67936

Other (OTH) AF: 0.602 AC: 1270 AN: 2110

Alfa AF: 0.630 Hom.: 94339

Bravo AF: 0.563

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1041834; hg19: chr21-42920022;