rs12629904

chr3-117511776-C-T

Variant summary

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

The XR_924361.3(LOC105374056):n.28456C>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 0.0528 in 152,006 control chromosomes in the GnomAD database, including 443 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 0.053 (443 hom., cov: 31)
• Consequence: LOC105374056 XR_924361.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374056	XR_924361.3	n.28456C>T		non_coding_transcript_exon_variant	1/4
LOC105374056	XR_007096021.1	n.28456C>T		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 8003 AN: 151888 Hom.: 442 Cov.: 31

Gnomad AFR AF: 0.0122

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0442

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

GnomAD4 genome AF: 0.0528 AC: 8019 AN: 152006 Hom.: 443 Cov.: 31 AF XY: 0.0591 AC XY: 4389 AN XY: 74286

Gnomad4 AFR AF: 0.0122

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.0572

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0459 Hom.: 125

Bravo AF: 0.0519

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.31
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12629904; hg19: chr3-117230623;