rs796184

Positions:

• chr13-89065176-C-T

Variant summary

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

The XR_001749951.2(LOC105370307):​n.148+18770C>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 0.154 in 151,696 control chromosomes in the GnomAD database, including 2,112 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 0.15 (2112 hom., cov: 32)
• Consequence: LOC105370307 XR_001749951.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

LOC105370307 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370307	XR_001749951.2	n.148+18770C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23317 AN: 151580 Hom.: 2112 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.154 AC: 23328 AN: 151696 Hom.: 2112 Cov.: 32 AF XY: 0.153 AC XY: 11368 AN XY: 74108

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.134

Alfa AF: 0.182 Hom.: 337

Bravo AF: 0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs796184; hg19: chr13-89717430;