rs13113697

Variant names:

• chr4-11709608-T-G
• rs13113697
• ENST00000510095.5:n.99-53851T>G

Variant summary

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

The ENST00000510095.5(ENSG00000249631):​n.99-53851T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,014 control chromosomes in the GnomAD database, including 36,145 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 0.69 (36145 hom., cov: 32)
• Consequence: ENSG00000249631 ENST00000510095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 3 publications found

Genes affected

ENSG00000249631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510095.5. 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
	LOC107986178	NR_188483.1		n.268-60701T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249631	ENST00000510095.5	TSL:3	n.99-53851T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104587 AN: 151896 Hom.: 36120 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.689 AC: 104674 AN: 152014 Hom.: 36145 Cov.: 32 AF XY: 0.686 AC XY: 50972 AN XY: 74314

African (AFR) AF: 0.668 AC: 27711 AN: 41462

American (AMR) AF: 0.635 AC: 9700 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3455 AN: 5172

South Asian (SAS) AF: 0.665 AC: 3207 AN: 4820

European-Finnish (FIN) AF: 0.685 AC: 7220 AN: 10544

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48682 AN: 67970

Other (OTH) AF: 0.701 AC: 1477 AN: 2108

Alfa AF: 0.689 Hom.: 4709

Bravo AF: 0.684

Asia WGS AF: 0.663 AC: 2302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.37
DANN	Benign	0.72
PhyloP100		-2.7

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: rs13113697;

hg19: chr4-11711232;