rs6593430

chr10-44607048-G-Achr10-44607048-G-Cchr10-44607048-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 0.876 in 152,104 control chromosomes in the GnomAD database, including 59,076 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 0.88 (59076 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.938 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: 0.876 AC: 133180 AN: 151986 Hom.: 59049 Cov.: 30

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.876 AC: 133261 AN: 152104 Hom.: 59076 Cov.: 30 AF XY: 0.878 AC XY: 65279 AN XY: 74362

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.896

Alfa AF: 0.923 Hom.: 25196

Bravo AF: 0.872

Asia WGS AF: 0.794 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.18
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6593430; hg19: chr10-45102496;