rs34809169

chr21-44982680-G-Achr21-44982680-G-T

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 0.146 in 152,286 control chromosomes in the GnomAD database, including 1,881 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 0.15 (1881 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22211 AN: 152168 Hom.: 1872 Cov.: 35

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22245 AN: 152286 Hom.: 1881 Cov.: 35 AF XY: 0.142 AC XY: 10544 AN XY: 74466

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.0862

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.151

Alfa AF: 0.0637 Hom.: 72

Bravo AF: 0.151

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34809169; hg19: chr21-46402595; COSMIC: COSV69383643;