chr15-56029404-T-C

Variant names:

• chr15-56029404-T-C
• rs7494783
• ENST00000737233.1:n.732-2364T>C

Variant summary

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

The ENST00000737233.1(ENSG00000296197):​n.732-2364T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 152,250 control chromosomes in the GnomAD database, including 599 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 0.078 (599 hom., cov: 32)
• Consequence: ENSG00000296197 ENST00000737233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 5 publications found

Genes affected

ENSG00000296197 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737233.1. 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
	ENSG00000296197	ENST00000737233.1		n.732-2364T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11882 AN: 152132 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0781 AC: 11887 AN: 152250 Hom.: 599 Cov.: 32 AF XY: 0.0768 AC XY: 5719 AN XY: 74438

African (AFR) AF: 0.0194 AC: 808 AN: 41568

American (AMR) AF: 0.0954 AC: 1458 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.0659 AC: 342 AN: 5186

South Asian (SAS) AF: 0.0468 AC: 226 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1081 AN: 10586

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7550 AN: 68008

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0980 Hom.: 508

Bravo AF: 0.0750

Asia WGS AF: 0.0550 AC: 192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.71
PhyloP100		-0.83

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: rs7494783;

hg19: chr15-56321602;