rs12460989

Positions:

• chr19-4785155-T-G

Variant summary

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

The ENST00000598782.2(ENSG00000268536):​n.494A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,846 control chromosomes in the GnomAD database, including 1,658 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 0.11 (1658 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000268536 ENST00000598782.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

ENSG00000268536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904620	XR_007067103.1	n.468A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000268536	ENST00000598782.2	n.494A>C		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16839 AN: 151740 Hom.: 1643 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0982

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.111 AC: 16904 AN: 151846 Hom.: 1658 Cov.: 32 AF XY: 0.110 AC XY: 8173 AN XY: 74210

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.0508

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0381

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.0808 Hom.: 131

Bravo AF: 0.121

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.22
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12460989; hg19: chr19-4785167;