rs2388399

Variant names:

• chr10-2750700-G-A
• rs2388399

Your query was ambiguous. Multiple possible variants found:

• chr10-2750700-G-A
• chr10-2750700-G-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 0.864 in 151,884 control chromosomes in the GnomAD database, including 59,477 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 (59477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 0.865 AC: 131219 AN: 151766 Hom.: 59453 Cov.: 31

Gnomad AFR AF: 0.559

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: 131293 AN: 151884 Hom.: 59477 Cov.: 31 AF XY: 0.871 AC XY: 64627 AN XY: 74234

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.991

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.905

Alfa AF: 0.910 Hom.: 8841

Bravo AF: 0.846

Asia WGS AF: 0.964 AC: 3343 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388399; hg19: chr10-2792892;