6-135144336-T-C

Variant names:

• chr6-135144336-T-C
• rs17064262

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 0.183 in 152,200 control chromosomes in the GnomAD database, including 2,582 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 (2582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.183 AC: 27767 AN: 152082 Hom.: 2585 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.183 AC: 27787 AN: 152200 Hom.: 2582 Cov.: 32 AF XY: 0.180 AC XY: 13430 AN XY: 74412

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.162

Alfa AF: 0.179 Hom.: 4998

Bravo AF: 0.181

Asia WGS AF: 0.139 AC: 483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17064262; hg19: chr6-135465474;