6-29685552-T-G

Variant names:

• chr6-29685552-T-G
• rs3117294

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 0.402 in 151,902 control chromosomes in the GnomAD database, including 13,348 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 0.40 (13348 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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: 0.402 AC: 60990 AN: 151784 Hom.: 13335 Cov.: 31

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.402 AC: 61048 AN: 151902 Hom.: 13348 Cov.: 31 AF XY: 0.397 AC XY: 29502 AN XY: 74230

African (AFR) AF: 0.558 AC: 23083 AN: 41376

American (AMR) AF: 0.462 AC: 7048 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5162

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4812

European-Finnish (FIN) AF: 0.200 AC: 2109 AN: 10544

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22757 AN: 67966

Other (OTH) AF: 0.449 AC: 946 AN: 2108

Alfa AF: 0.360 Hom.: 38757

Bravo AF: 0.433

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3117294; hg19: chr6-29653329;