rs12881353

chr14-64896897-A-Gchr14-64896897-A-T

Variant summary

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

The XR_943942.3(LOC105370534):n.57+5175T>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 0.531 in 104,178 control chromosomes in the GnomAD database, including 21,063 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 0.53 (21063 hom., cov: 26)
• Consequence: LOC105370534 XR_943942.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

LOC105370534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370534	XR_943942.3	n.57+5175T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.531 AC: 55300 AN: 104060 Hom.: 21063 Cov.: 26

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.531 AC: 55307 AN: 104178 Hom.: 21063 Cov.: 26 AF XY: 0.528 AC XY: 26870 AN XY: 50850

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.576

Alfa AF: 0.710 Hom.: 15369

Bravo AF: 0.562

Asia WGS AF: 0.314 AC: 798 AN: 2540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	10
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12881353; hg19: chr14-65363615;