rs7314734

Positions:

• chr12-49946258-C-T

Variant summary

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

The XR_944942.3(LOC105369763):​n.2539C>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 0.0936 in 152,170 control chromosomes in the GnomAD database, including 1,336 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 0.094 (1336 hom., cov: 33)
• Consequence: LOC105369763 XR_944942.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

LOC105369763 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369763	XR_001749129.2	n.2897C>T		non_coding_transcript_exon_variant	2/3
LOC105369763	XR_001749130.2	n.2691C>T		non_coding_transcript_exon_variant	3/4
LOC105369763	XR_001749132.2	n.2733C>T		non_coding_transcript_exon_variant	3/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14214 AN: 152052 Hom.: 1326 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0936 AC: 14246 AN: 152170 Hom.: 1336 Cov.: 33 AF XY: 0.0950 AC XY: 7068 AN XY: 74394

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0171

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0721 Hom.: 252

Bravo AF: 0.109

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7314734; hg19: chr12-50340041;