8-141060879-C-T

Position:

• chr8-141060879-C-T

Variant summary

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

The XR_002956733.2(LOC105375784):​n.1213C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,060 control chromosomes in the GnomAD database, including 9,349 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 0.34 (9349 hom., cov: 33)
• Consequence: LOC105375784 XR_002956733.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

LOC105375784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375784	XR_002956733.2	n.1213C>T		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52007 AN: 151942 Hom.: 9335 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.342 AC: 52061 AN: 152060 Hom.: 9349 Cov.: 33 AF XY: 0.344 AC XY: 25543 AN XY: 74322

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.348

Alfa AF: 0.321 Hom.: 2087

Bravo AF: 0.342

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1078671; hg19: chr8-142070978;