13-58671029-G-C

Position:

• chr13-58671029-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_941985.2(LOC105370219):​n.115-11730C>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 0.19 in 151,582 control chromosomes in the GnomAD database, including 3,237 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 0.19 (3237 hom., cov: 32)
• Consequence: LOC105370219 XR_941985.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

Genes affected

LOC105370219 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370219	XR_941985.2	n.115-11730C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28732 AN: 151464 Hom.: 3230 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.190 AC: 28751 AN: 151582 Hom.: 3237 Cov.: 32 AF XY: 0.195 AC XY: 14411 AN XY: 74070

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.201

Alfa AF: 0.0907 Hom.: 127

Bravo AF: 0.188

Asia WGS AF: 0.391 AC: 1357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	13
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1537473; hg19: chr13-59245163;