10-2750700-G-A

Variant names:

• chr10-2750700-G-A
• rs2388399

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 151,884 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.865 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

African (AFR) AF: 0.559 AC: 23060 AN: 41274

American (AMR) AF: 0.929 AC: 14188 AN: 15270

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

East Asian (EAS) AF: 0.978 AC: 5052 AN: 5164

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

European-Finnish (FIN) AF: 0.998 AC: 10560 AN: 10582

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

European-Non Finnish (NFE) AF: 0.989 AC: 67228 AN: 68000

Other (OTH) AF: 0.905 AC: 1902 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2388399; hg19: chr10-2792892;