chr9-133629444-G-A

Variant names:

• chr9-133629444-G-A
• rs2519148
• ENST00000564021.1:n.113+3543C>T

Variant summary

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

The ENST00000564021.1(ENSG00000261018):​n.113+3543C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,898 control chromosomes in the GnomAD database, including 16,426 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 0.46 (16426 hom., cov: 32)
• Consequence: ENSG00000261018 ENST00000564021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 6 publications found

Genes affected

ENSG00000261018 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 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
ENSG00000261018	ENST00000564021.1	n.113+3543C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70073 AN: 151780 Hom.: 16412 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.462 AC: 70114 AN: 151898 Hom.: 16426 Cov.: 32 AF XY: 0.464 AC XY: 34428 AN XY: 74214

African (AFR) AF: 0.381 AC: 15771 AN: 41416

American (AMR) AF: 0.480 AC: 7341 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1800 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2187 AN: 5142

South Asian (SAS) AF: 0.565 AC: 2717 AN: 4806

European-Finnish (FIN) AF: 0.495 AC: 5244 AN: 10586

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33341 AN: 67890

Other (OTH) AF: 0.459 AC: 968 AN: 2110

Alfa AF: 0.484 Hom.: 58499

Bravo AF: 0.458

Asia WGS AF: 0.485 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2519148; hg19: chr9-136494566;