rs12589672

chr14-36524701-A-T

Variant summary

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

The XR_001750715.2(LOC105370453):n.13A>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 0.0423 in 152,112 control chromosomes in the GnomAD database, including 206 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 0.042 (206 hom., cov: 33)
• Consequence: LOC105370453 XR_001750715.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC105370453 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370453	XR_001750715.2	n.13A>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634305.1	n.322+75864A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6425 AN: 151994 Hom.: 207 Cov.: 33

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0423 AC: 6428 AN: 152112 Hom.: 206 Cov.: 33 AF XY: 0.0441 AC XY: 3280 AN XY: 74360

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0401 Hom.: 19

Bravo AF: 0.0438

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.80
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12589672; hg19: chr14-36993906;