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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.918

Alfa AF: 0.919 Hom.: 22395

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750829; hg19: chr10-132547261;