rs2388399

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;