rs2832626

Positions:

• chr21-30105161-T-G
• chr21-30105161-T-C

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 0.173 in 152,054 control chromosomes in the GnomAD database, including 2,654 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 0.17 (2654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.173 AC: 26237 AN: 151936 Hom.: 2652 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.173 AC: 26257 AN: 152054 Hom.: 2654 Cov.: 32 AF XY: 0.170 AC XY: 12617 AN XY: 74348

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.160

Alfa AF: 0.109 Hom.: 320

Bravo AF: 0.179

Asia WGS AF: 0.230 AC: 798 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832626; hg19: chr21-31477479;