chr2-74344955-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000264324 (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 = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451608.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264324	ENST00000451608.2	TSL:5	n.*240-2418A>G		intron	N/A	ENSP00000416453.2
	ENSG00000301222	ENST00000777098.1		n.150+1293T>C		intron	N/A

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

African (AFR) AF: 0.395 AC: 16377 AN: 41424

American (AMR) AF: 0.146 AC: 2225 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2433 AN: 5166

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4816

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10588

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7646 AN: 67984

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.154 Hom.: 959

Bravo AF: 0.224

Asia WGS AF: 0.356 AC: 1234 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	8.2
DANN	Benign	0.72
PhyloP100		0.20

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

Other links and lift over

dbSNP: rs6732913; hg19: chr2-74572082;