rs4750829

Variant names:

• chr10-130748997-A-G
• rs4750829

Your query was ambiguous. Multiple possible variants found:

• chr10-130748997-A-G
• chr10-130748997-A-T

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 0.906 in 152,194 control chromosomes in the GnomAD database, including 62,743 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 (62743 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.94 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: 0.906 AC: 137813 AN: 152076 Hom.: 62714 Cov.: 34

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.906 AC: 137894 AN: 152194 Hom.: 62743 Cov.: 34 AF XY: 0.907 AC XY: 67483 AN XY: 74420

African (AFR) AF: 0.822 AC: 34092 AN: 41484

American (AMR) AF: 0.887 AC: 13582 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3388 AN: 3470

East Asian (EAS) AF: 0.940 AC: 4871 AN: 5180

South Asian (SAS) AF: 0.953 AC: 4601 AN: 4828

European-Finnish (FIN) AF: 0.933 AC: 9874 AN: 10588

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.946 AC: 64365 AN: 68024

Other (OTH) AF: 0.918 AC: 1935 AN: 2108

Alfa AF: 0.926 Hom.: 114048

Bravo AF: 0.897

Asia WGS AF: 0.933 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.24
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4750829; hg19: chr10-132547261;