rs2832768

Variant names:

• chr21-30295561-G-A
• rs2832768

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 0.173 in 151,966 control chromosomes in the GnomAD database, including 2,963 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 (2963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.173 AC: 26246 AN: 151848 Hom.: 2959 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.173 AC: 26270 AN: 151966 Hom.: 2963 Cov.: 32 AF XY: 0.170 AC XY: 12633 AN XY: 74298

African (AFR) AF: 0.311 AC: 12862 AN: 41404

American (AMR) AF: 0.146 AC: 2235 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3468

East Asian (EAS) AF: 0.0956 AC: 494 AN: 5170

South Asian (SAS) AF: 0.133 AC: 640 AN: 4826

European-Finnish (FIN) AF: 0.0689 AC: 727 AN: 10546

Middle Eastern (MID) AF: 0.163 AC: 47 AN: 288

European-Non Finnish (NFE) AF: 0.119 AC: 8085 AN: 67962

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.159 Hom.: 416

Bravo AF: 0.185

Asia WGS AF: 0.122 AC: 424 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.24
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2832768; hg19: chr21-31667879;