rs12053481

chr2-18651080-C-Achr2-18651080-C-G

Variant summary

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

The XR_007086234.1(LOC105373456):n.853+6780C>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 0.137 in 152,028 control chromosomes in the GnomAD database, including 2,084 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 0.14 (2084 hom., cov: 32)
• Consequence: LOC105373456 XR_007086234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

Genes affected

LOC105373456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373456	XR_007086234.1	n.853+6780C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20801 AN: 151910 Hom.: 2078 Cov.: 32

Gnomad AFR AF: 0.0410

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.137 AC: 20823 AN: 152028 Hom.: 2084 Cov.: 32 AF XY: 0.139 AC XY: 10351 AN XY: 74302

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.0879

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.170

Alfa AF: 0.156 Hom.: 4234

Bravo AF: 0.149

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12053481; hg19: chr2-18832346;