rs6732758

Variant names:

• chr2-174745231-G-A
• rs6732758
• ENST00000442996.1:n.321+15407G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-174745231-G-A
• chr2-174745231-G-C
• chr2-174745231-G-T

Variant summary

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

The ENST00000442996.1(ENSG00000236449):​n.321+15407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,132 control chromosomes in the GnomAD database, including 45,403 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 0.76 (45403 hom., cov: 33)
• Consequence: ENSG00000236449 ENST00000442996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 publications found

Genes affected

ENSG00000236449 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442996.1. 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
	ENSG00000236449	ENST00000442996.1	TSL:1	n.321+15407G>A		intron	N/A
	ENSG00000236449	ENST00000842848.1		n.398G>A		non_coding_transcript_exon	Exon 4 of 5
	ENSG00000236449	ENST00000842845.1		n.326+15407G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115449 AN: 152014 Hom.: 45390 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.759 AC: 115499 AN: 152132 Hom.: 45403 Cov.: 33 AF XY: 0.763 AC XY: 56767 AN XY: 74390

African (AFR) AF: 0.531 AC: 22012 AN: 41436

American (AMR) AF: 0.852 AC: 13021 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2757 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4597 AN: 5190

South Asian (SAS) AF: 0.724 AC: 3491 AN: 4820

European-Finnish (FIN) AF: 0.897 AC: 9509 AN: 10604

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57506 AN: 68004

Other (OTH) AF: 0.755 AC: 1593 AN: 2110

Alfa AF: 0.753 Hom.: 8931

Bravo AF: 0.748

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.57
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs6732758; hg19: chr2-175609959;