rs7318572

Variant names:

• chr13-23104796-T-A
• rs7318572
• ENST00000743290.1:n.228+3293A>T

Your query was ambiguous. Multiple possible variants found:

• chr13-23104796-T-A
• chr13-23104796-T-C

Variant summary

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

The ENST00000743290.1(ENSG00000296879):​n.228+3293A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,256 control chromosomes in the GnomAD database, including 400 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 0.052 (400 hom., cov: 32)
• Consequence: ENSG00000296879 ENST00000743290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 2 publications found

Genes affected

ENSG00000296879 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743290.1. 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
	ENSG00000296879	ENST00000743290.1		n.228+3293A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0515 AC: 7832 AN: 152138 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.0310

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

GnomAD4 genome AF: 0.0516 AC: 7861 AN: 152256 Hom.: 400 Cov.: 32 AF XY: 0.0534 AC XY: 3972 AN XY: 74438

African (AFR) AF: 0.113 AC: 4677 AN: 41530

American (AMR) AF: 0.0188 AC: 288 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3472

East Asian (EAS) AF: 0.153 AC: 792 AN: 5170

South Asian (SAS) AF: 0.102 AC: 493 AN: 4816

European-Finnish (FIN) AF: 0.0159 AC: 169 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0189 AC: 1287 AN: 68034

Other (OTH) AF: 0.0345 AC: 73 AN: 2116

Alfa AF: 0.0361 Hom.: 24

Bravo AF: 0.0528

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs7318572; hg19: chr13-23678935;