chr6-113141177-C-T

Variant names:

• chr6-113141177-C-T
• rs2502397

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 0.43 in 151,880 control chromosomes in the GnomAD database, including 14,311 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 0.43 (14311 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.430 AC: 65248 AN: 151762 Hom.: 14298 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.430 AC: 65302 AN: 151880 Hom.: 14311 Cov.: 31 AF XY: 0.433 AC XY: 32146 AN XY: 74264

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.437

Alfa AF: 0.417 Hom.: 1678

Bravo AF: 0.431

Asia WGS AF: 0.391 AC: 1360 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	0.66
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2502397; hg19: chr6-113462379; COSMIC: COSV69420641;