chr12-121087863-G-A

Position:

• chr12-121087863-G-A

Variant summary

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

The XR_007063492.1(LOC105378258):​n.5133C>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 0.0702 in 152,206 control chromosomes in the GnomAD database, including 619 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 0.070 (619 hom., cov: 32)
• Consequence: LOC105378258 XR_007063492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

LOC105378258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378258	XR_007063492.1	n.5133C>T		non_coding_transcript_exon_variant	1/4
LOC105378258	XR_945451.4	n.5133C>T		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10678 AN: 152088 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.0155

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0702 AC: 10682 AN: 152206 Hom.: 619 Cov.: 32 AF XY: 0.0722 AC XY: 5371 AN XY: 74410

Gnomad4 AFR AF: 0.0155

Gnomad4 AMR AF: 0.0421

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0924

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.0963

Gnomad4 OTH AF: 0.0641

Alfa AF: 0.0913 Hom.: 361

Bravo AF: 0.0551

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492051; hg19: chr12-121525666;