rs1548039

Variant names:

• chr2-120361345-A-C
• rs1548039

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 0.325 in 152,176 control chromosomes in the GnomAD database, including 12,496 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 0.32 (12496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.324 AC: 49322 AN: 152060 Hom.: 12465 Cov.: 33

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.325 AC: 49411 AN: 152176 Hom.: 12496 Cov.: 33 AF XY: 0.327 AC XY: 24317 AN XY: 74426

African (AFR) AF: 0.690 AC: 28652 AN: 41508

American (AMR) AF: 0.295 AC: 4514 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2647 AN: 5158

South Asian (SAS) AF: 0.356 AC: 1715 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1503 AN: 10608

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9126 AN: 67990

Other (OTH) AF: 0.270 AC: 572 AN: 2116

Alfa AF: 0.195 Hom.: 17918

Bravo AF: 0.352

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.33
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1548039; hg19: chr2-121118921;