rs501548

Positions:

• chr2-173567350-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;