rs12607243

Positions:

• chr18-30395264-A-G

Variant summary

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

The ENST00000657542.1(ENSG00000286605):​n.528-17363A>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 0.0303 in 152,226 control chromosomes in the GnomAD database, including 91 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 0.030 (91 hom., cov: 32)
• Consequence: ENST00000657542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0791 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
	ENST00000657542.1	n.528-17363A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4625 AN: 152108 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.0239

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0303 AC: 4619 AN: 152226 Hom.: 91 Cov.: 32 AF XY: 0.0306 AC XY: 2275 AN XY: 74428

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0857

Gnomad4 SAS AF: 0.0540

Gnomad4 FIN AF: 0.0239

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.0298 Hom.: 12

Bravo AF: 0.0322

Asia WGS AF: 0.0880 AC: 304 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12607243; hg19: chr18-27975230;