rs1548039

Variant names:

• chr2-120361345-A-C
• rs1548039

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.270

Alfa AF: 0.166 Hom.: 4597

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1548039; hg19: chr2-121118921;