rs1526929

Variant names:

• chr3-135336868-C-G
• rs1526929
• ENST00000649588.1:n.108-75809G>C

Variant summary

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

The ENST00000649588.1(ENSG00000240086):​n.108-75809G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,042 control chromosomes in the GnomAD database, including 6,308 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 0.28 (6308 hom., cov: 32)
• Consequence: ENSG00000240086 ENST00000649588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 1 publications found

Genes affected

ENSG00000240086 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000240086	ENST00000649588.1	n.108-75809G>C		intron_variant	Intron 1 of 6
ENSG00000240086	ENST00000655873.1	n.366+42394G>C		intron_variant	Intron 3 of 3
ENSG00000240086	ENST00000815171.1	n.122-75809G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42809 AN: 151924 Hom.: 6308 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.282 AC: 42819 AN: 152042 Hom.: 6308 Cov.: 32 AF XY: 0.278 AC XY: 20637 AN XY: 74308

African (AFR) AF: 0.359 AC: 14900 AN: 41448

American (AMR) AF: 0.320 AC: 4889 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 963 AN: 3472

East Asian (EAS) AF: 0.155 AC: 804 AN: 5184

South Asian (SAS) AF: 0.202 AC: 974 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2120 AN: 10560

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17365 AN: 67978

Other (OTH) AF: 0.272 AC: 574 AN: 2112

Alfa AF: 0.269 Hom.: 717

Bravo AF: 0.292

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.70
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1526929; hg19: chr3-135055710;