rs12153243

Variant names:

• chr5-143520236-A-T
• rs12153243
• ENST00000340585.6:n.437+10678T>A

Variant summary

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

The ENST00000340585.6(ENSG00000249429):​n.437+10678T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,888 control chromosomes in the GnomAD database, including 9,950 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 0.36 (9950 hom., cov: 32)
• Consequence: ENSG00000249429 ENST00000340585.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 10 publications found

Genes affected

ENSG00000249429 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 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
ENSG00000249429	ENST00000340585.6	n.437+10678T>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54219 AN: 151770 Hom.: 9949 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.357 AC: 54244 AN: 151888 Hom.: 9950 Cov.: 32 AF XY: 0.359 AC XY: 26661 AN XY: 74238

African (AFR) AF: 0.347 AC: 14351 AN: 41396

American (AMR) AF: 0.288 AC: 4400 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1096 AN: 5164

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4812

European-Finnish (FIN) AF: 0.472 AC: 4972 AN: 10524

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25092 AN: 67928

Other (OTH) AF: 0.356 AC: 751 AN: 2110

Alfa AF: 0.360 Hom.: 1324

Bravo AF: 0.342

Asia WGS AF: 0.264 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12153243; hg19: chr5-142899801;