rs1519592

Variant names:

• chr6-140222499-T-C
• rs1519592
• ENST00000683950.1:n.201+73809T>C

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.201+73809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,034 control chromosomes in the GnomAD database, including 2,675 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 (2675 hom., cov: 32)
• Consequence: ENSG00000288714 ENST00000683950.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 4 publications found

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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
ENSG00000288714	ENST00000683950.1	n.201+73809T>C		intron_variant	Intron 1 of 1
ENSG00000288714	ENST00000825769.1	n.175+73809T>C		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25782 AN: 151916 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.0651

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.170 AC: 25790 AN: 152034 Hom.: 2675 Cov.: 32 AF XY: 0.170 AC XY: 12653 AN XY: 74310

African (AFR) AF: 0.0652 AC: 2706 AN: 41534

American (AMR) AF: 0.199 AC: 3041 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2106 AN: 5154

South Asian (SAS) AF: 0.159 AC: 764 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2290 AN: 10522

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13507 AN: 67962

Other (OTH) AF: 0.171 AC: 361 AN: 2110

Alfa AF: 0.172 Hom.: 322

Bravo AF: 0.166

Asia WGS AF: 0.267 AC: 925 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.79
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1519592; hg19: chr6-140543636;