rs12637032

chr3-867062-A-G

Variant summary

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

The XR_001740584.1(LOC107986058):n.8094-2897A>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 0.367 in 152,054 control chromosomes in the GnomAD database, including 10,449 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 (10449 hom., cov: 32)
• Consequence: LOC107986058 XR_001740584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

LOC107986058 (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 = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986058	XR_001740584.1	n.8094-2897A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55790 AN: 151936 Hom.: 10454 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.367 AC: 55812 AN: 152054 Hom.: 10449 Cov.: 32 AF XY: 0.372 AC XY: 27618 AN XY: 74308

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.367

Alfa AF: 0.338 Hom.: 1482

Bravo AF: 0.368

Asia WGS AF: 0.499 AC: 1732 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	0.72
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12637032; hg19: chr3-908745;