rs2388395

Variant names:

• chr10-2750458-A-G
• rs2388395

Your query was ambiguous. Multiple possible variants found:

• chr10-2750458-A-G
• chr10-2750458-A-T

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 0.908 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.908 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

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.993

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.943

Alfa AF: 0.972 Hom.: 37675

Bravo AF: 0.896

Asia WGS AF: 0.977 AC: 3394 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388395; hg19: chr10-2792650;