rs12819930

chr12-121087788-G-Achr12-121087788-G-T

Variant summary

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

The XR_007063492.1(LOC105378258):n.5208C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,206 control chromosomes in the GnomAD database, including 388 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 0.060 (388 hom., cov: 32)
• Consequence: LOC105378258 XR_007063492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

Genes affected

LOC105378258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378258	XR_007063492.1	n.5208C>T		non_coding_transcript_exon_variant	1/4
LOC105378258	XR_945451.4	n.5208C>T		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9147 AN: 152088 Hom.: 388 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0799

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0601 AC: 9148 AN: 152206 Hom.: 388 Cov.: 32 AF XY: 0.0603 AC XY: 4489 AN XY: 74410

Gnomad4 AFR AF: 0.0157

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.0536

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.0799

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0663 Hom.: 175

Bravo AF: 0.0578

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	9.3
Dann	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12819930; hg19: chr12-121525591;