13-47324744-A-G

Variant names:

• chr13-47324744-A-G
• rs1417205
• ENST00000751481.1:n.159-73385T>C

Variant summary

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

The ENST00000751481.1(ENSG00000297874):​n.159-73385T>C 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 152,008 control chromosomes in the GnomAD database, including 2,156 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 (2156 hom., cov: 32)
• Consequence: ENSG00000297874 ENST00000751481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634
• Publications: 8 publications found

Genes affected

ENSG00000297874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751481.1. 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
	ENSG00000297874	ENST00000751481.1		n.159-73385T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19169 AN: 151890 Hom.: 2157 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19187 AN: 152008 Hom.: 2156 Cov.: 32 AF XY: 0.125 AC XY: 9261 AN XY: 74332

African (AFR) AF: 0.300 AC: 12433 AN: 41428

American (AMR) AF: 0.0929 AC: 1418 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0655 AC: 227 AN: 3466

East Asian (EAS) AF: 0.0569 AC: 294 AN: 5170

South Asian (SAS) AF: 0.107 AC: 516 AN: 4818

European-Finnish (FIN) AF: 0.0464 AC: 491 AN: 10590

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0516 AC: 3505 AN: 67968

Other (OTH) AF: 0.113 AC: 239 AN: 2108

Alfa AF: 0.0740 Hom.: 1951

Bravo AF: 0.136

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.89
PhyloP100		0.63

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: rs1417205;

hg19: chr13-47898879;