rs6714954

Variant names:

• chr2-74344876-G-C
• rs6714954
• ENST00000451608.2:n.*240-2339C>G

Variant summary

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

The ENST00000451608.2(ENSG00000264324):​n.*240-2339C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,214 control chromosomes in the GnomAD database, including 1,611 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 0.13 (1611 hom., cov: 32)
• Consequence: ENSG00000264324 ENST00000451608.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 7 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=-0.9).
• 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264324	ENST00000451608.2	TSL:5	n.*240-2339C>G		intron	N/A	ENSP00000416453.2	E7EWF7
	ENSG00000301222	ENST00000777098.1		n.150+1214G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19164 AN: 152096 Hom.: 1609 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.126 AC: 19171 AN: 152214 Hom.: 1611 Cov.: 32 AF XY: 0.129 AC XY: 9623 AN XY: 74418

African (AFR) AF: 0.121 AC: 5013 AN: 41536

American (AMR) AF: 0.106 AC: 1626 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2441 AN: 5182

South Asian (SAS) AF: 0.207 AC: 999 AN: 4828

European-Finnish (FIN) AF: 0.102 AC: 1079 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7115 AN: 68012

Other (OTH) AF: 0.132 AC: 277 AN: 2104

Alfa AF: 0.107 Hom.: 132

Bravo AF: 0.128

Asia WGS AF: 0.330 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		-0.026

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: rs6714954; hg19: chr2-74572003;