rs325105

Variant names:

• chr6-147443131-C-T
• rs325105

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 0.294 in 151,880 control chromosomes in the GnomAD database, including 8,112 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 0.29 (8112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 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: 0.295 AC: 44716 AN: 151762 Hom.: 8114 Cov.: 31

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.294 AC: 44706 AN: 151880 Hom.: 8112 Cov.: 31 AF XY: 0.294 AC XY: 21831 AN XY: 74204

African (AFR) AF: 0.0751 AC: 3109 AN: 41414

American (AMR) AF: 0.327 AC: 4982 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1697 AN: 5156

South Asian (SAS) AF: 0.285 AC: 1369 AN: 4806

European-Finnish (FIN) AF: 0.356 AC: 3747 AN: 10530

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27287 AN: 67946

Other (OTH) AF: 0.339 AC: 716 AN: 2110

Alfa AF: 0.369 Hom.: 18635

Bravo AF: 0.282

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs325105; hg19: chr6-147764267;