rs1163849

Positions:

• chr13-111435586-T-A
• chr13-111435586-T-G

Variant summary

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

The XR_001750032.2(LOC107984618):​n.595-15366T>A 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 0.828 in 152,062 control chromosomes in the GnomAD database, including 53,478 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 0.83 (53478 hom., cov: 31)
• Consequence: LOC107984618 XR_001750032.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

LOC107984618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984618	XR_001750032.2	n.595-15366T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125891 AN: 151944 Hom.: 53456 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.828 AC: 125962 AN: 152062 Hom.: 53478 Cov.: 31 AF XY: 0.834 AC XY: 61962 AN XY: 74334

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.833

Alfa AF: 0.858 Hom.: 7057

Bravo AF: 0.815

Asia WGS AF: 0.855 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163849; hg19: chr13-112087933;