rs12459249

chr19-40833991-T-C

Variant summary

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

The ENST00000596135.1(ENSG00000269843):n.126-2414A>G 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 0.66 in 151,734 control chromosomes in the GnomAD database, including 33,291 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 0.66 (33291 hom., cov: 31)
• Consequence: ENST00000596135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000596135.1	n.126-2414A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100049 AN: 151616 Hom.: 33258 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.660 AC: 100140 AN: 151734 Hom.: 33291 Cov.: 31 AF XY: 0.658 AC XY: 48778 AN XY: 74184

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.651

Alfa AF: 0.664 Hom.: 4183

Bravo AF: 0.659

Asia WGS AF: 0.547 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12459249; hg19: chr19-41339896;