10-2750671-A-T

Variant names:

• chr10-2750671-A-T
• rs2388397

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 0.864 in 151,982 control chromosomes in the GnomAD database, including 59,500 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 0.86 (59500 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.982 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: 0.864 AC: 131268 AN: 151864 Hom.: 59476 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.864 AC: 131342 AN: 151982 Hom.: 59500 Cov.: 31 AF XY: 0.870 AC XY: 64659 AN XY: 74284

African (AFR) AF: 0.558 AC: 23096 AN: 41356

American (AMR) AF: 0.929 AC: 14179 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5053 AN: 5166

South Asian (SAS) AF: 0.991 AC: 4773 AN: 4814

European-Finnish (FIN) AF: 0.998 AC: 10580 AN: 10602

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67225 AN: 67998

Other (OTH) AF: 0.905 AC: 1906 AN: 2106

Alfa AF: 0.905 Hom.: 3412

Bravo AF: 0.846

Asia WGS AF: 0.964 AC: 3342 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2388397; hg19: chr10-2792863;