10-6066377-A-G

Position:

• chr10-6066377-A-G

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 0.404 in 151,940 control chromosomes in the GnomAD database, including 13,221 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 0.40 (13221 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.404 AC: 61349 AN: 151824 Hom.: 13200 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.404 AC: 61411 AN: 151940 Hom.: 13221 Cov.: 31 AF XY: 0.414 AC XY: 30748 AN XY: 74254

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.413

Alfa AF: 0.410 Hom.: 2520

Bravo AF: 0.395

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10795791; hg19: chr10-6108340;