rs12052359

Positions:

• chr2-81645798-C-A
• chr2-81645798-C-T

Variant summary

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

The XR_007088668.1(LOC102724542):​n.667+66189C>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 0.225 in 151,628 control chromosomes in the GnomAD database, including 4,862 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 0.22 (4862 hom., cov: 32)
• Consequence: LOC102724542 XR_007088668.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

LOC102724542 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724542	XR_007088668.1	n.667+66189C>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940294.2	n.575+66189C>A		intron_variant, non_coding_transcript_variant
LOC102724542	XR_940295.2	n.497+97051C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34099 AN: 151512 Hom.: 4858 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.225 AC: 34107 AN: 151628 Hom.: 4862 Cov.: 32 AF XY: 0.229 AC XY: 16939 AN XY: 74064

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.275

Alfa AF: 0.274 Hom.: 10860

Bravo AF: 0.233

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12052359; hg19: chr2-81872922;