rs1498759

Positions:

• chr12-115386277-C-T

Variant summary

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

The XR_945389.3(LOC105370003):​n.503-12390G>A 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 0.369 in 151,616 control chromosomes in the GnomAD database, including 10,643 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 0.37 (10643 hom., cov: 31)
• Consequence: LOC105370003 XR_945389.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

LOC105370003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370003	XR_945389.3	n.503-12390G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55912 AN: 151500 Hom.: 10637 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.369 AC: 55937 AN: 151616 Hom.: 10643 Cov.: 31 AF XY: 0.371 AC XY: 27510 AN XY: 74062

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.387

Alfa AF: 0.383 Hom.: 3435

Bravo AF: 0.356

Asia WGS AF: 0.457 AC: 1585 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1498759; hg19: chr12-115824082;