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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374523	XR_001741614.1	n.227-21266C>T		intron_variant	Intron 1 of 2
LOC105374524	XR_007058437.1	n.2933-11172G>A		intron_variant	Intron 16 of 18
LOC105374523	XR_925460.2	n.227-21266C>T		intron_variant	Intron 1 of 2
LOC105374523	XR_925461.2	n.266-21266C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298732	ENST00000757640.1	n.285-21266C>T		intron_variant	Intron 1 of 4
ENSG00000298732	ENST00000757641.1	n.268-21266C>T		intron_variant	Intron 1 of 3
ENSG00000298732	ENST00000757642.1	n.253-21266C>T		intron_variant	Intron 1 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs13143346; hg19: chr4-23352332;