rs1519529

Variant names:

• chr2-136216687-C-G
• rs1519529
• ENST00000805101.1:n.686-12288C>G

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.686-12288C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,196 control chromosomes in the GnomAD database, including 3,130 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 (3130 hom., cov: 32)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 5 publications found

Genes affected

ENSG00000304642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 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
ENSG00000304642	ENST00000805101.1	n.686-12288C>G		intron_variant	Intron 1 of 1
ENSG00000304642	ENST00000805103.1	n.179+2220C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26459 AN: 152078 Hom.: 3129 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.174 AC: 26459 AN: 152196 Hom.: 3130 Cov.: 32 AF XY: 0.170 AC XY: 12621 AN XY: 74410

African (AFR) AF: 0.0495 AC: 2056 AN: 41548

American (AMR) AF: 0.175 AC: 2678 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5188

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4814

European-Finnish (FIN) AF: 0.146 AC: 1551 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17493 AN: 67982

Other (OTH) AF: 0.178 AC: 375 AN: 2110

Alfa AF: 0.190 Hom.: 440

Bravo AF: 0.166

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.39
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1519529; hg19: chr2-136974257;