8-27591212-T-C

Variant names:

• chr8-27591212-T-C
• rs7012010
• XR_007060868.1:n.-4T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060868.1(LOC124901919):​n.-4T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,138 control chromosomes in the GnomAD database, including 6,492 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 0.29 (6492 hom., cov: 33)
• Consequence: LOC124901919 XR_007060868.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 23 publications found

Genes affected

LOC124901919 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43989 AN: 152020 Hom.: 6488 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.289 AC: 44026 AN: 152138 Hom.: 6492 Cov.: 33 AF XY: 0.287 AC XY: 21362 AN XY: 74376

African (AFR) AF: 0.303 AC: 12594 AN: 41522

American (AMR) AF: 0.290 AC: 4436 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.387 AC: 1996 AN: 5164

South Asian (SAS) AF: 0.369 AC: 1772 AN: 4806

European-Finnish (FIN) AF: 0.180 AC: 1908 AN: 10576

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19020 AN: 67996

Other (OTH) AF: 0.292 AC: 616 AN: 2110

Alfa AF: 0.282 Hom.: 10366

Bravo AF: 0.298

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.36
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7012010; hg19: chr8-27448729;