rs2519148

Positions:

• chr9-133629444-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564021.1(ENSG00000261018):​n.113+3543C>T variant causes a intron, non coding transcript 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: ENST00000564021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000564021.1	n.113+3543C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.459

Alfa AF: 0.492 Hom.: 36961

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2519148; hg19: chr9-136494566;