rs12829697

chr12-30023023-A-Gchr12-30023023-A-T

Variant summary

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

The XR_931474.1(LOC105369715):n.135-9093T>C 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 0.102 in 152,212 control chromosomes in the GnomAD database, including 1,055 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 0.10 (1055 hom., cov: 32)
• Consequence: LOC105369715 XR_931474.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

Genes affected

LOC105369715 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369715	XR_931474.1	n.135-9093T>C		intron_variant, non_coding_transcript_variant
LOC105369715	XR_001749060.1	n.135-9093T>C		intron_variant, non_coding_transcript_variant
LOC105369715	XR_001749061.1	n.135-9093T>C		intron_variant, non_coding_transcript_variant
LOC105369715	XR_931476.1	n.135-9093T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15508 AN: 152094 Hom.: 1055 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.102 AC: 15505 AN: 152212 Hom.: 1055 Cov.: 32 AF XY: 0.104 AC XY: 7727 AN XY: 74412

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.112

Alfa AF: 0.108 Hom.: 152

Bravo AF: 0.0986

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.8
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12829697; hg19: chr12-30175956;