rs744186

Variant names:

• chr13-103195603-G-T
• rs744186
• ENST00000741727.1:n.104+26391G>T

Variant summary

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

The ENST00000741727.1(ENSG00000296764):​n.104+26391G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 151,634 control chromosomes in the GnomAD database, including 382 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 0.045 (382 hom., cov: 33)
• Consequence: ENSG00000296764 ENST00000741727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 1 publications found

Genes affected

ENSG00000296764 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741727.1. 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
	ENSG00000296764	ENST00000741727.1		n.104+26391G>T		intron	N/A
	ENSG00000296764	ENST00000741728.1		n.99+26391G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6828 AN: 151518 Hom.: 381 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.00907

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0370

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

GnomAD4 genome AF: 0.0451 AC: 6837 AN: 151634 Hom.: 382 Cov.: 33 AF XY: 0.0437 AC XY: 3240 AN XY: 74072

African (AFR) AF: 0.132 AC: 5460 AN: 41298

American (AMR) AF: 0.0255 AC: 388 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3462

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4798

European-Finnish (FIN) AF: 0.00907 AC: 95 AN: 10470

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 742 AN: 67912

Other (OTH) AF: 0.0361 AC: 76 AN: 2104

Alfa AF: 0.0351 Hom.: 29

Bravo AF: 0.0497

Asia WGS AF: 0.00953 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.14

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: rs744186;

hg19: chr13-103847953;