rs501548

Variant names:

• chr2-173567350-G-A
• rs501548

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 0.596 in 151,962 control chromosomes in the GnomAD database, including 27,397 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 0.60 (27397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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: 0.596 AC: 90514 AN: 151844 Hom.: 27384 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.596 AC: 90559 AN: 151962 Hom.: 27397 Cov.: 32 AF XY: 0.588 AC XY: 43687 AN XY: 74274

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.612

Alfa AF: 0.629 Hom.: 29140

Bravo AF: 0.590

Asia WGS AF: 0.494 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.76
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs501548; hg19: chr2-174432078;