13-109606435-T-G

Position:

• chr13-109606435-T-G

Variant summary

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

The XR_007063870.1(LOC124903210):​n.714A>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 0.288 in 152,196 control chromosomes in the GnomAD database, including 7,514 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 0.29 (7514 hom., cov: 33)
• Consequence: LOC124903210 XR_007063870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660

Genes affected

LOC124903210 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903210	XR_007063870.1	n.714A>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-35277A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43825 AN: 152078 Hom.: 7512 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.288 AC: 43825 AN: 152196 Hom.: 7514 Cov.: 33 AF XY: 0.284 AC XY: 21158 AN XY: 74402

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.299

Alfa AF: 0.318 Hom.: 1393

Bravo AF: 0.277

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9515085; hg19: chr13-110258782;