rs1546079

Variant names:

• chr3-46108627-C-T
• rs1546079

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 0.429 in 151,960 control chromosomes in the GnomAD database, including 17,165 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 0.43 (17165 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 7 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 (SAS) allele frequency at 95% confidence interval = 0.694 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: 0.430 AC: 65231 AN: 151842 Hom.: 17150 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.429 AC: 65253 AN: 151960 Hom.: 17165 Cov.: 32 AF XY: 0.443 AC XY: 32890 AN XY: 74256

African (AFR) AF: 0.118 AC: 4890 AN: 41416

American (AMR) AF: 0.541 AC: 8263 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1891 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3669 AN: 5170

South Asian (SAS) AF: 0.713 AC: 3436 AN: 4816

European-Finnish (FIN) AF: 0.592 AC: 6240 AN: 10538

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35232 AN: 67964

Other (OTH) AF: 0.459 AC: 964 AN: 2102

Alfa AF: 0.473 Hom.: 7970

Bravo AF: 0.402

Asia WGS AF: 0.693 AC: 2409 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	0.30
DANN	Benign	0.72
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1546079; hg19: chr3-46150119;