13-109801260-G-T

Variant names:

• chr13-109801260-G-T
• rs7986346
• ENST00000615635.1:n.116-5797G>T

Variant summary

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

The ENST00000615635.1(ENSG00000275741):​n.116-5797G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,128 control chromosomes in the GnomAD database, including 52,254 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 0.83 (52254 hom., cov: 33)
• Consequence: ENSG00000275741 ENST00000615635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 11 publications found

Genes affected

ENSG00000275741 (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 (AMR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615635.1. 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
	ENSG00000275741	ENST00000615635.1	TSL:4	n.116-5797G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125847 AN: 152010 Hom.: 52206 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.828 AC: 125952 AN: 152128 Hom.: 52254 Cov.: 33 AF XY: 0.828 AC XY: 61566 AN XY: 74364

African (AFR) AF: 0.820 AC: 34006 AN: 41460

American (AMR) AF: 0.860 AC: 13159 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2984 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3500 AN: 5168

South Asian (SAS) AF: 0.776 AC: 3744 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 8988 AN: 10586

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56827 AN: 67996

Other (OTH) AF: 0.821 AC: 1736 AN: 2114

Alfa AF: 0.833 Hom.: 28571

Bravo AF: 0.829

Asia WGS AF: 0.730 AC: 2504 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.41
PhyloP100		-0.52

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: rs7986346;

hg19: chr13-110453607;