rs3129109

Variant names:

• chr6-29116455-T-C
• rs3129109

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 0.446 in 147,748 control chromosomes in the GnomAD database, including 17,604 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 0.45 (17604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 50 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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: 0.446 AC: 65869 AN: 147650 Hom.: 17593 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.446 AC: 65877 AN: 147748 Hom.: 17604 Cov.: 32 AF XY: 0.444 AC XY: 32117 AN XY: 72266

African (AFR) AF: 0.130 AC: 4984 AN: 38422

American (AMR) AF: 0.456 AC: 6807 AN: 14926

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1467 AN: 3410

East Asian (EAS) AF: 0.352 AC: 1804 AN: 5120

South Asian (SAS) AF: 0.401 AC: 1900 AN: 4736

European-Finnish (FIN) AF: 0.637 AC: 6671 AN: 10474

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.604 AC: 40732 AN: 67390

Other (OTH) AF: 0.414 AC: 857 AN: 2068

Alfa AF: 0.545 Hom.: 82354

Bravo AF: 0.401

Asia WGS AF: 0.426 AC: 1483 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	5.5
DANN	Benign	0.66
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs3129109; hg19: chr6-29084232;