rs1380232

chr8-76046714-C-G

Variant summary

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

The XR_929059.3(LOC105375906):n.4052+1317G>C 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 0.0928 in 152,042 control chromosomes in the GnomAD database, including 985 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 0.093 (985 hom., cov: 32)
• Consequence: LOC105375906 XR_929059.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

Genes affected

LOC105375906 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375906	XR_929059.3	n.4052+1317G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14068 AN: 151924 Hom.: 979 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0390

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0928 AC: 14105 AN: 152042 Hom.: 985 Cov.: 32 AF XY: 0.0916 AC XY: 6805 AN XY: 74326

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0384

Gnomad4 FIN AF: 0.0212

Gnomad4 NFE AF: 0.0405

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0686 Hom.: 73

Bravo AF: 0.108

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1380232; hg19: chr8-76958949;