13-37461052-C-T

Variant summary

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

The XR_007063761.1(LOC124903159):n.244-17553C>T 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 0.206 in 152,038 control chromosomes in the GnomAD database, including 4,373 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 0.21 (4373 hom., cov: 32)
• Consequence: LOC124903159 XR_007063761.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

LOC124903159 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903159	XR_007063761.1	n.244-17553C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31234 AN: 151920 Hom.: 4367 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.206 AC: 31266 AN: 152038 Hom.: 4373 Cov.: 32 AF XY: 0.209 AC XY: 15531 AN XY: 74340

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.186

Alfa AF: 0.128 Hom.: 1925

Bravo AF: 0.219

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.2
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1590305; hg19: chr13-38035189;