21-42311295-G-A

Variant names:

• chr21-42311295-G-A
• rs225439

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 0.487 in 150,776 control chromosomes in the GnomAD database, including 18,512 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 0.49 (18512 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73407 AN: 150656 Hom.: 18492 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.487 AC: 73476 AN: 150776 Hom.: 18512 Cov.: 31 AF XY: 0.480 AC XY: 35314 AN XY: 73634

African (AFR) AF: 0.613 AC: 24951 AN: 40724

American (AMR) AF: 0.441 AC: 6688 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1631 AN: 3464

East Asian (EAS) AF: 0.209 AC: 1076 AN: 5158

South Asian (SAS) AF: 0.386 AC: 1799 AN: 4664

European-Finnish (FIN) AF: 0.383 AC: 3995 AN: 10434

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31714 AN: 67860

Other (OTH) AF: 0.464 AC: 972 AN: 2094

Alfa AF: 0.472 Hom.: 28739

Bravo AF: 0.494

Asia WGS AF: 0.296 AC: 1022 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.040
DANN	Benign	0.41
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs225439; hg19: chr21-43731405;