rs912969

Variant names:

• chr13-103214754-C-T
• rs912969
• ENST00000741727.1:n.104+45542C>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+45542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,094 control chromosomes in the GnomAD database, including 3,776 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 0.17 (3776 hom., cov: 32)
• Consequence: ENSG00000296764 ENST00000741727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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+45542C>T		intron	N/A
	ENSG00000296764	ENST00000741728.1		n.99+45542C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26071 AN: 151978 Hom.: 3762 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.172 AC: 26128 AN: 152094 Hom.: 3776 Cov.: 32 AF XY: 0.168 AC XY: 12495 AN XY: 74374

African (AFR) AF: 0.382 AC: 15841 AN: 41452

American (AMR) AF: 0.145 AC: 2223 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1293 AN: 5156

South Asian (SAS) AF: 0.116 AC: 559 AN: 4812

European-Finnish (FIN) AF: 0.0469 AC: 497 AN: 10596

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0749 AC: 5093 AN: 68010

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.109 Hom.: 5270

Bravo AF: 0.190

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		-0.28

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: rs912969;

hg19: chr13-103867104;