rs13116075

Variant names:

• chr4-139008878-A-G
• rs13116075
• ENST00000511951.2:n.374+3717T>C

Variant summary

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

The ENST00000511951.2(ENSG00000250195):​n.374+3717T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,264 control chromosomes in the GnomAD database, including 1,176 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 0.11 (1176 hom., cov: 32)
• Consequence: ENSG00000250195 ENST00000511951.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 11 publications found

Genes affected

ENSG00000250195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511951.2. 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
	LOC105377448	NR_133945.1		n.52+3717T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250195	ENST00000511951.2	TSL:3	n.374+3717T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16834 AN: 152146 Hom.: 1177 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.111 AC: 16829 AN: 152264 Hom.: 1176 Cov.: 32 AF XY: 0.109 AC XY: 8117 AN XY: 74438

African (AFR) AF: 0.0378 AC: 1572 AN: 41578

American (AMR) AF: 0.100 AC: 1528 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0830 AC: 400 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1825 AN: 10606

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10643 AN: 67996

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.140 Hom.: 3071

Bravo AF: 0.102

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.50
PhyloP100		-0.83

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: rs13116075;

hg19: chr4-139930032;