rs10518609

Variant names:

• chr4-132330899-G-T
• rs10518609
• ENST00000652009.1:n.177+4822C>A

Variant summary

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

The ENST00000652009.1(ENSG00000251598):​n.177+4822C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,092 control chromosomes in the GnomAD database, including 3,338 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 0.20 (3338 hom., cov: 33)
• Consequence: ENSG00000251598 ENST00000652009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 0 publications found

Genes affected

ENSG00000251598 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 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
ENSG00000251598	ENST00000652009.1	n.177+4822C>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30464 AN: 151974 Hom.: 3332 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.200 AC: 30492 AN: 152092 Hom.: 3338 Cov.: 33 AF XY: 0.199 AC XY: 14831 AN XY: 74370

African (AFR) AF: 0.126 AC: 5227 AN: 41508

American (AMR) AF: 0.219 AC: 3352 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.0917 AC: 475 AN: 5180

South Asian (SAS) AF: 0.193 AC: 928 AN: 4814

European-Finnish (FIN) AF: 0.250 AC: 2645 AN: 10572

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16336 AN: 67956

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.228 Hom.: 1961

Bravo AF: 0.196

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10518609; hg19: chr4-133252054;