chr6-115807742-C-T

Variant names:

• chr6-115807742-C-T
• rs10485114

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 0.234 in 152,000 control chromosomes in the GnomAD database, including 4,365 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 0.23 (4365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 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: 0.234 AC: 35597 AN: 151880 Hom.: 4360 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.234 AC: 35620 AN: 152000 Hom.: 4365 Cov.: 32 AF XY: 0.231 AC XY: 17165 AN XY: 74308

African (AFR) AF: 0.199 AC: 8241 AN: 41466

American (AMR) AF: 0.191 AC: 2909 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4810

European-Finnish (FIN) AF: 0.183 AC: 1931 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17914 AN: 67942

Other (OTH) AF: 0.234 AC: 494 AN: 2114

Alfa AF: 0.240 Hom.: 2493

Bravo AF: 0.230

Asia WGS AF: 0.246 AC: 854 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.043
DANN	Benign	0.36
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10485114; hg19: chr6-116128906; COSMIC: COSV69421683;