6-6341054-A-C

Variant names:

• chr6-6341054-A-C
• rs17142067

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 0.231 in 152,176 control chromosomes in the GnomAD database, including 5,075 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 (5075 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 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: 0.231 AC: 35180 AN: 152058 Hom.: 5079 Cov.: 33

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.231 AC: 35156 AN: 152176 Hom.: 5075 Cov.: 33 AF XY: 0.229 AC XY: 17015 AN XY: 74386

African (AFR) AF: 0.0658 AC: 2736 AN: 41582

American (AMR) AF: 0.191 AC: 2926 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2097 AN: 5182

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4818

European-Finnish (FIN) AF: 0.263 AC: 2770 AN: 10548

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21713 AN: 67970

Other (OTH) AF: 0.239 AC: 505 AN: 2112

Alfa AF: 0.276 Hom.: 9882

Bravo AF: 0.221

Asia WGS AF: 0.302 AC: 1048 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.055
DANN	Benign	0.77
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17142067; hg19: chr6-6341287;