rs41295065

Variant names:

• chr10-6075012-G-A
• rs41295065

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 0.0598 in 152,260 control chromosomes in the GnomAD database, including 395 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 0.060 (395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0895 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: 0.0599 AC: 9108 AN: 152142 Hom.: 394 Cov.: 31

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0598 AC: 9108 AN: 152260 Hom.: 395 Cov.: 31 AF XY: 0.0579 AC XY: 4308 AN XY: 74450

African (AFR) AF: 0.0172 AC: 714 AN: 41548

American (AMR) AF: 0.0399 AC: 611 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0533 AC: 257 AN: 4820

European-Finnish (FIN) AF: 0.0637 AC: 676 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0914 AC: 6218 AN: 68010

Other (OTH) AF: 0.0517 AC: 109 AN: 2110

Alfa AF: 0.0682 Hom.: 57

Bravo AF: 0.0571

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs41295065; hg19: chr10-6116975;