chr8-117377370-C-T

Position:

• chr8-117377370-C-T

Variant summary

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

The XR_007061067.1(LOC105375716):​n.559+63590G>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 0.205 in 151,774 control chromosomes in the GnomAD database, including 4,064 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 0.20 (4064 hom., cov: 32)
• Consequence: LOC105375716 XR_007061067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

Genes affected

LOC105375716 (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 (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375716	XR_007061067.1	n.559+63590G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31105 AN: 151656 Hom.: 4065 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.205 AC: 31088 AN: 151774 Hom.: 4064 Cov.: 32 AF XY: 0.205 AC XY: 15194 AN XY: 74172

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.194

Alfa AF: 0.261 Hom.: 3452

Bravo AF: 0.187

Asia WGS AF: 0.214 AC: 744 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	5.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1695718; hg19: chr8-118389609;