rs501548

Variant names:

• chr2-173567350-G-A
• rs501548
• ENST00000737367.1:n.391+34011G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000737367.1(ENSG00000270460):​n.391+34011G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000270460 ENST00000737367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 2 publications found

Genes affected

ENSG00000270460 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737367.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270460	ENST00000737367.1		n.391+34011G>A		intron	N/A
	ENSG00000270460	ENST00000737368.1		n.518+34011G>A		intron	N/A
	ENSG00000270460	ENST00000737369.1		n.503+34011G>A		intron	N/A

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

African (AFR) AF: 0.603 AC: 24987 AN: 41454

American (AMR) AF: 0.505 AC: 7705 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2412 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1769 AN: 5140

South Asian (SAS) AF: 0.596 AC: 2863 AN: 4800

European-Finnish (FIN) AF: 0.544 AC: 5742 AN: 10554

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43008 AN: 67962

Other (OTH) AF: 0.612 AC: 1287 AN: 2104

Alfa AF: 0.624 Hom.: 37857

Bravo AF: 0.590

Asia WGS AF: 0.494 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.76
DANN	Benign	0.54
PhyloP100		-0.084

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs501548;

hg19: chr2-174432078;