21-42597842-T-G

Variant names:

• chr21-42597842-T-G
• rs401809

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 0.678 in 149,896 control chromosomes in the GnomAD database, including 35,249 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 0.68 (35249 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 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: 0.678 AC: 101487 AN: 149778 Hom.: 35235 Cov.: 25

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.678 AC: 101559 AN: 149896 Hom.: 35249 Cov.: 25 AF XY: 0.673 AC XY: 49159 AN XY: 73022

African (AFR) AF: 0.600 AC: 24291 AN: 40470

American (AMR) AF: 0.771 AC: 11644 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2387 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1020 AN: 5062

South Asian (SAS) AF: 0.605 AC: 2865 AN: 4734

European-Finnish (FIN) AF: 0.717 AC: 7187 AN: 10022

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 49846 AN: 67746

Other (OTH) AF: 0.685 AC: 1432 AN: 2092

Alfa AF: 0.698 Hom.: 24807

Bravo AF: 0.677

Asia WGS AF: 0.433 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs401809; hg19: chr21-44017952;