rs13143346

Variant names:

• chr4-23350709-G-A
• rs13143346
• ENST00000757640.1:n.285-21266C>T

Variant summary

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

The ENST00000757640.1(ENSG00000298732):​n.285-21266C>T 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 152,178 control chromosomes in the GnomAD database, including 522 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 (522 hom., cov: 32)
• Consequence: ENSG00000298732 ENST00000757640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0855 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.285-21266C>T		intron	N/A
	ENSG00000298732	ENST00000757641.1		n.268-21266C>T		intron	N/A
	ENSG00000298732	ENST00000757642.1		n.253-21266C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12440 AN: 152060 Hom.: 521 Cov.: 32

Gnomad AFR AF: 0.0819

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0578

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0818 AC: 12443 AN: 152178 Hom.: 522 Cov.: 32 AF XY: 0.0814 AC XY: 6054 AN XY: 74390

African (AFR) AF: 0.0818 AC: 3395 AN: 41528

American (AMR) AF: 0.0596 AC: 911 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0578 AC: 200 AN: 3462

East Asian (EAS) AF: 0.0415 AC: 215 AN: 5178

South Asian (SAS) AF: 0.0840 AC: 405 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1092 AN: 10576

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

European-Non Finnish (NFE) AF: 0.0873 AC: 5939 AN: 68002

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.0841 Hom.: 326

Bravo AF: 0.0788

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.55
PhyloP100		-1.5

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: rs13143346;

hg19: chr4-23352332;