rs401809

Positions:

• chr21-42597842-T-G
• chr21-42597842-T-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.685

Alfa AF: 0.710 Hom.: 16812

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs401809; hg19: chr21-44017952;