rs7294500

Variant names:

• chr12-33272747-G-A
• rs7294500
• ENST00000849294.1:n.392-5558C>T

Variant summary

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

The ENST00000849294.1(ENSG00000310362):​n.392-5558C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 151,550 control chromosomes in the GnomAD database, including 954 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 0.082 (954 hom., cov: 31)
• Consequence: ENSG00000310362 ENST00000849294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 2 publications found

Genes affected

ENSG00000310362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849294.1. 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
	ENSG00000310362	ENST00000849294.1		n.392-5558C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0819 AC: 12398 AN: 151432 Hom.: 953 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0724

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

GnomAD4 genome AF: 0.0819 AC: 12405 AN: 151550 Hom.: 954 Cov.: 31 AF XY: 0.0802 AC XY: 5939 AN XY: 74092

African (AFR) AF: 0.203 AC: 8402 AN: 41302

American (AMR) AF: 0.0509 AC: 771 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5146

South Asian (SAS) AF: 0.0429 AC: 206 AN: 4802

European-Finnish (FIN) AF: 0.0425 AC: 445 AN: 10476

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0310 AC: 2102 AN: 67880

Other (OTH) AF: 0.0716 AC: 151 AN: 2108

Alfa AF: 0.0507 Hom.: 1137

Bravo AF: 0.0889

Asia WGS AF: 0.0250 AC: 88 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.29
PhyloP100		0.079

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7294500;

hg19: chr12-33425682;