10-32250511-A-G

Variant names:

• chr10-32250511-A-G
• rs2769234

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 0.442 in 150,630 control chromosomes in the GnomAD database, including 17,555 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 0.44 (17555 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66505 AN: 150542 Hom.: 17518 Cov.: 29

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.442 AC: 66584 AN: 150630 Hom.: 17555 Cov.: 29 AF XY: 0.436 AC XY: 31990 AN XY: 73412

African (AFR) AF: 0.750 AC: 30700 AN: 40942

American (AMR) AF: 0.360 AC: 5449 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1773 AN: 5138

South Asian (SAS) AF: 0.320 AC: 1522 AN: 4750

European-Finnish (FIN) AF: 0.299 AC: 3016 AN: 10096

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.320 AC: 21676 AN: 67790

Other (OTH) AF: 0.415 AC: 870 AN: 2094

Alfa AF: 0.422 Hom.: 4521

Bravo AF: 0.465

Asia WGS AF: 0.311 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2769234; hg19: chr10-32539439; COSMIC: COSV68663356;