6-113597448-C-T

Variant names:

• chr6-113597448-C-T
• rs7755236

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 0.182 in 152,192 control chromosomes in the GnomAD database, including 2,931 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 0.18 (2931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 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: 0.182 AC: 27706 AN: 152074 Hom.: 2928 Cov.: 32

Gnomad AFR AF: 0.0743

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.182 AC: 27723 AN: 152192 Hom.: 2931 Cov.: 32 AF XY: 0.186 AC XY: 13857 AN XY: 74392

African (AFR) AF: 0.0743 AC: 3089 AN: 41548

American (AMR) AF: 0.192 AC: 2931 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4816

European-Finnish (FIN) AF: 0.194 AC: 2060 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15564 AN: 68008

Other (OTH) AF: 0.198 AC: 420 AN: 2116

Alfa AF: 0.205 Hom.: 2156

Bravo AF: 0.173

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7755236; hg19: chr6-113918650;