rs13151220

Variant names:

• chr4-23344726-G-T
• rs13151220
• ENST00000757640.1:n.285-15283C>A

Variant summary

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

The ENST00000757640.1(ENSG00000298732):​n.285-15283C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,148 control chromosomes in the GnomAD database, including 526 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 (526 hom., cov: 32)
• Consequence: ENSG00000298732 ENST00000757640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 2 publications found

Genes affected

ENSG00000298732 (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 (NFE) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757640.1. 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
	ENSG00000298732	ENST00000757640.1		n.285-15283C>A		intron	N/A
	ENSG00000298732	ENST00000757641.1		n.268-15283C>A		intron	N/A
	ENSG00000298732	ENST00000757642.1		n.253-15283C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12437 AN: 152030 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0818 AC: 12439 AN: 152148 Hom.: 526 Cov.: 32 AF XY: 0.0814 AC XY: 6056 AN XY: 74382

African (AFR) AF: 0.0817 AC: 3394 AN: 41538

American (AMR) AF: 0.0595 AC: 909 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3470

East Asian (EAS) AF: 0.0407 AC: 210 AN: 5164

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4828

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10596

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5931 AN: 67962

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0835 Hom.: 966

Bravo AF: 0.0789

Asia WGS AF: 0.0930 AC: 322 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.62
PhyloP100		0.68

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: rs13151220;

hg19: chr4-23346349;