rs12473173

chr2-195128876-C-Achr2-195128876-C-T

Variant summary

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

The XR_007088699.1(LOC105376755):n.197-69373G>T 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 0.0845 in 152,142 control chromosomes in the GnomAD database, including 571 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 0.084 (571 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

LOC105376755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376755	XR_007088699.1	n.197-69373G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12844 AN: 152024 Hom.: 571 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0845 AC: 12855 AN: 152142 Hom.: 571 Cov.: 32 AF XY: 0.0839 AC XY: 6238 AN XY: 74354

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0825

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.0607

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0728 Hom.: 620

Bravo AF: 0.0901

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.74
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: rs12473173; hg19: chr2-195993600;