10-6359663-C-T

Variant names:

• chr10-6359663-C-T
• rs4558075

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 0.817 in 151,484 control chromosomes in the GnomAD database, including 50,614 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 0.82 (50614 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.817 AC: 123630 AN: 151372 Hom.: 50572 Cov.: 30

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.817 AC: 123724 AN: 151484 Hom.: 50614 Cov.: 30 AF XY: 0.820 AC XY: 60667 AN XY: 74002

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.818

Alfa AF: 0.815 Hom.: 84109

Bravo AF: 0.818

Asia WGS AF: 0.907 AC: 3130 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4558075; hg19: chr10-6401625;