13-47324960-A-G

Variant names:

• chr13-47324960-A-G
• rs564425
• ENST00000751481.1:n.159-73601T>C

Variant summary

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

The ENST00000751481.1(ENSG00000297874):​n.159-73601T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,976 control chromosomes in the GnomAD database, including 20,169 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 0.48 (20169 hom., cov: 31)
• Consequence: ENSG00000297874 ENST00000751481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297874	ENST00000751481.1	n.159-73601T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72595 AN: 151858 Hom.: 20177 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.478 AC: 72598 AN: 151976 Hom.: 20169 Cov.: 31 AF XY: 0.477 AC XY: 35425 AN XY: 74280

African (AFR) AF: 0.174 AC: 7211 AN: 41490

American (AMR) AF: 0.626 AC: 9547 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2337 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2237 AN: 5164

South Asian (SAS) AF: 0.460 AC: 2218 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5600 AN: 10528

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41689 AN: 67952

Other (OTH) AF: 0.516 AC: 1088 AN: 2108

Alfa AF: 0.567 Hom.: 16666

Bravo AF: 0.473

Asia WGS AF: 0.447 AC: 1553 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs564425; hg19: chr13-47899095;