rs401074

Variant names:

• chr21-42593381-A-G
• rs401074

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 0.742 in 152,240 control chromosomes in the GnomAD database, including 42,800 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 0.74 (42800 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 4 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 = 0.811 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: 0.742 AC: 112865 AN: 152122 Hom.: 42759 Cov.: 34

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.742 AC: 112972 AN: 152240 Hom.: 42800 Cov.: 34 AF XY: 0.735 AC XY: 54730 AN XY: 74436

African (AFR) AF: 0.819 AC: 34015 AN: 41552

American (AMR) AF: 0.795 AC: 12167 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1139 AN: 5162

South Asian (SAS) AF: 0.620 AC: 2999 AN: 4834

European-Finnish (FIN) AF: 0.721 AC: 7649 AN: 10604

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50163 AN: 67994

Other (OTH) AF: 0.729 AC: 1538 AN: 2110

Alfa AF: 0.732 Hom.: 24121

Bravo AF: 0.749

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.40
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs401074; hg19: chr21-44013491;