10-2750458-A-G

Variant names:

• chr10-2750458-A-G
• rs2388395

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 0.908 in 152,268 control chromosomes in the GnomAD database, including 64,078 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 0.91 (64078 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138216 AN: 152150 Hom.: 64047 Cov.: 33

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.908 AC: 138305 AN: 152268 Hom.: 64078 Cov.: 33 AF XY: 0.914 AC XY: 68019 AN XY: 74456

African (AFR) AF: 0.699 AC: 29005 AN: 41504

American (AMR) AF: 0.959 AC: 14682 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3467 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5175 AN: 5176

South Asian (SAS) AF: 0.993 AC: 4788 AN: 4822

European-Finnish (FIN) AF: 0.998 AC: 10605 AN: 10626

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.991 AC: 67410 AN: 68044

Other (OTH) AF: 0.943 AC: 1991 AN: 2112

Alfa AF: 0.976 Hom.: 55911

Bravo AF: 0.896

Asia WGS AF: 0.977 AC: 3394 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2388395; hg19: chr10-2792650;