rs747273

chr14-77260635-G-C

Variant summary

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

The XR_007064276.1(LOC124903351):n.817G>C 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 0.34 in 152,212 control chromosomes in the GnomAD database, including 10,559 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 0.34 (10559 hom., cov: 34)
• Consequence: LOC124903351 XR_007064276.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

LOC124903351 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903351	XR_007064276.1	n.817G>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51680 AN: 152094 Hom.: 10558 Cov.: 34

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.340 AC: 51684 AN: 152212 Hom.: 10559 Cov.: 34 AF XY: 0.342 AC XY: 25448 AN XY: 74394

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.347

Alfa AF: 0.413 Hom.: 1805

Bravo AF: 0.311

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747273; hg19: chr14-77726978;