rs13116912

Variant names:

• chr4-110251341-A-C
• rs13116912
• ENST00000833186.1:n.152-618A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-110251341-A-C
• chr4-110251341-A-T

Variant summary

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

The ENST00000833186.1(ENSG00000308313):​n.152-618A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,266 control chromosomes in the GnomAD database, including 593 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 0.061 (593 hom., cov: 32)
• Consequence: ENSG00000308313 ENST00000833186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 2 publications found

Genes affected

ENSG00000308313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833186.1. 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
	ENSG00000308313	ENST00000833186.1		n.152-618A>C		intron	N/A
	ENSG00000308313	ENST00000833187.1		n.345+545A>C		intron	N/A
	ENSG00000308313	ENST00000833188.1		n.307+545A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9253 AN: 152148 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0240

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0609 AC: 9268 AN: 152266 Hom.: 593 Cov.: 32 AF XY: 0.0590 AC XY: 4393 AN XY: 74452

African (AFR) AF: 0.154 AC: 6405 AN: 41538

American (AMR) AF: 0.0396 AC: 606 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3472

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5182

South Asian (SAS) AF: 0.00746 AC: 36 AN: 4826

European-Finnish (FIN) AF: 0.0191 AC: 202 AN: 10596

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0240 AC: 1633 AN: 68034

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0305 Hom.: 100

Bravo AF: 0.0684

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.71
PhyloP100		0.044

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: rs13116912;

hg19: chr4-111172497;