13-23118952-T-C

Position:

• chr13-23118952-T-C

Variant summary

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

The XR_001749786.1(LOC105370112):​n.426-810A>G 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 0.892 in 152,174 control chromosomes in the GnomAD database, including 61,388 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 0.89 (61388 hom., cov: 31)
• Consequence: LOC105370112 XR_001749786.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

LOC105370112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370112	XR_001749786.1	n.426-810A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135711 AN: 152056 Hom.: 61366 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.892 AC: 135783 AN: 152174 Hom.: 61388 Cov.: 31 AF XY: 0.890 AC XY: 66189 AN XY: 74408

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.918

Alfa AF: 0.942 Hom.: 31788

Bravo AF: 0.881

Asia WGS AF: 0.771 AC: 2684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7322449; hg19: chr13-23693091;