rs13028485

Variant names:

• chr2-173640196-G-A
• rs13028485
• ENST00000737367.1:n.391+106857G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-173640196-G-A
• chr2-173640196-G-C
• chr2-173640196-G-T

Variant summary

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

The ENST00000737367.1(ENSG00000270460):​n.391+106857G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 152,202 control chromosomes in the GnomAD database, including 548 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 0.080 (548 hom., cov: 33)
• Consequence: ENSG00000270460 ENST00000737367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000270460	ENST00000737367.1		n.391+106857G>A		intron	N/A
	ENSG00000270460	ENST00000737368.1		n.518+106857G>A		intron	N/A
	ENSG00000270460	ENST00000737369.1		n.503+106857G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12221 AN: 152082 Hom.: 546 Cov.: 33

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0694

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0805 AC: 12246 AN: 152202 Hom.: 548 Cov.: 33 AF XY: 0.0809 AC XY: 6018 AN XY: 74424

African (AFR) AF: 0.0926 AC: 3845 AN: 41514

American (AMR) AF: 0.0824 AC: 1260 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0694 AC: 241 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5168

South Asian (SAS) AF: 0.108 AC: 522 AN: 4824

European-Finnish (FIN) AF: 0.0470 AC: 498 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4626 AN: 68010

Other (OTH) AF: 0.0806 AC: 170 AN: 2108

Alfa AF: 0.0742 Hom.: 1454

Bravo AF: 0.0821

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.70
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs13028485; hg19: chr2-174504924;