rs1078671

Variant names:

• chr8-141060879-C-T
• rs1078671
• XR_002956733.2:n.1213C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC105375784 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.399 AC: 16548 AN: 41450

American (AMR) AF: 0.284 AC: 4336 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3334 AN: 5158

South Asian (SAS) AF: 0.408 AC: 1967 AN: 4824

European-Finnish (FIN) AF: 0.305 AC: 3235 AN: 10590

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20495 AN: 67976

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.333 Hom.: 3788

Bravo AF: 0.342

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.59
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1078671; hg19: chr8-142070978;