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. Variant got -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

Genes affected

ENSG00000236449 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000236449	ENST00000442996.1	n.321+15407G>A		intron_variant	Intron 3 of 3	1

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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.755

Alfa AF: 0.758 Hom.: 8819

Bravo AF: 0.748

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6732758; hg19: chr2-175609959;