10-6082658-T-C

Variant names:

• chr10-6082658-T-C
• rs41295115

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 0.0479 in 152,314 control chromosomes in the GnomAD database, including 204 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 0.048 (204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0571 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7293 AN: 152196 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.0590

Gnomad EAS AF: 0.00134

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0479 AC: 7296 AN: 152314 Hom.: 204 Cov.: 32 AF XY: 0.0485 AC XY: 3612 AN XY: 74478

African (AFR) AF: 0.0392 AC: 1629 AN: 41552

American (AMR) AF: 0.0600 AC: 917 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 205 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5194

South Asian (SAS) AF: 0.0630 AC: 304 AN: 4828

European-Finnish (FIN) AF: 0.0441 AC: 468 AN: 10620

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3572 AN: 68036

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0467 Hom.: 54

Bravo AF: 0.0482

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.89
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs41295115; hg19: chr10-6124621;