chr10-6066377-A-G

Variant names:

• chr10-6066377-A-G
• rs10795791

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 41 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.276 AC: 11416 AN: 41426

American (AMR) AF: 0.516 AC: 7863 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2901 AN: 5178

South Asian (SAS) AF: 0.533 AC: 2568 AN: 4816

European-Finnish (FIN) AF: 0.544 AC: 5738 AN: 10550

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28514 AN: 67952

Other (OTH) AF: 0.413 AC: 866 AN: 2098

Alfa AF: 0.408 Hom.: 2556

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
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10795791; hg19: chr10-6108340;