13-106132916-T-C

Variant names:

• chr13-106132916-T-C
• rs1372791
• ENST00000754737.1:n.129-42122A>G

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.129-42122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,316 control chromosomes in the GnomAD database, including 68,147 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 0.94 (68147 hom., cov: 34)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 7 publications found

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754737.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287923	ENST00000754737.1		n.129-42122A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143674 AN: 152198 Hom.: 68100 Cov.: 34

Gnomad AFR AF: 0.842

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.944 AC: 143778 AN: 152316 Hom.: 68147 Cov.: 34 AF XY: 0.946 AC XY: 70448 AN XY: 74482

African (AFR) AF: 0.842 AC: 34967 AN: 41550

American (AMR) AF: 0.974 AC: 14911 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3400 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5171 AN: 5172

South Asian (SAS) AF: 0.990 AC: 4780 AN: 4826

European-Finnish (FIN) AF: 0.992 AC: 10544 AN: 10630

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66786 AN: 68038

Other (OTH) AF: 0.954 AC: 2019 AN: 2116

Alfa AF: 0.969 Hom.: 221621

Bravo AF: 0.938

Asia WGS AF: 0.984 AC: 3422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.65
PhyloP100		0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1372791; hg19: chr13-106785265;