rs1529276

Variant names:

• chr13-103275657-T-A
• rs1529276
• ENST00000741727.1:n.105-20349T>A

Variant summary

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

The ENST00000741727.1(ENSG00000296764):​n.105-20349T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,254 control chromosomes in the GnomAD database, including 1,605 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 0.13 (1605 hom., cov: 32)
• Consequence: ENSG00000296764 ENST00000741727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 19 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296764	ENST00000741727.1	n.105-20349T>A		intron_variant	Intron 1 of 3
ENSG00000296764	ENST00000741728.1	n.100-20349T>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19956 AN: 152136 Hom.: 1606 Cov.: 32

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.0701

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.131 AC: 19953 AN: 152254 Hom.: 1605 Cov.: 32 AF XY: 0.123 AC XY: 9143 AN XY: 74454

African (AFR) AF: 0.0724 AC: 3008 AN: 41556

American (AMR) AF: 0.130 AC: 1995 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.0119 AC: 62 AN: 5190

South Asian (SAS) AF: 0.0699 AC: 337 AN: 4820

European-Finnish (FIN) AF: 0.0680 AC: 721 AN: 10606

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12792 AN: 68002

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.171 Hom.: 1367

Bravo AF: 0.136

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1529276; hg19: chr13-103928007; COSMIC: COSV63536065;