10-6000071-C-T

Variant names:

• chr10-6000071-C-T
• rs10795731

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 0.942 in 152,238 control chromosomes in the GnomAD database, including 67,595 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 0.94 (67595 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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: 0.942 AC: 143306 AN: 152120 Hom.: 67535 Cov.: 31

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.942 AC: 143424 AN: 152238 Hom.: 67595 Cov.: 31 AF XY: 0.940 AC XY: 69998 AN XY: 74434

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.945

Alfa AF: 0.948 Hom.: 9639

Bravo AF: 0.945

Asia WGS AF: 0.964 AC: 3353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10795731; hg19: chr10-6042034;