rs6732913

Variant names:

• chr2-74344955-T-C
• rs6732913
• ENST00000451608.2:n.*240-2418A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451608.2(ENSG00000264324):​n.*240-2418A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,046 control chromosomes in the GnomAD database, including 4,748 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 0.21 (4748 hom., cov: 32)
• Consequence: ENSG00000264324 ENST00000451608.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

ENSG00000264324 (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 = 0.455 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
ENSG00000264324	ENST00000451608.2	n.*240-2418A>G		intron_variant	Intron 6 of 38	5		ENSP00000416453.2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31917 AN: 151928 Hom.: 4739 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.210 AC: 31958 AN: 152046 Hom.: 4748 Cov.: 32 AF XY: 0.210 AC XY: 15600 AN XY: 74334

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.191

Alfa AF: 0.150 Hom.: 770

Bravo AF: 0.224

Asia WGS AF: 0.356 AC: 1234 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	8.2
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6732913; hg19: chr2-74572082;