8-11792966-T-C

Variant names:

• chr8-11792966-T-C
• rs7001819
• XR_948962.4:n.44-4899A>G

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-4899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,100 control chromosomes in the GnomAD database, including 9,394 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 0.35 (9394 hom., cov: 33)
• Consequence: LOC105379243 XR_948962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 16 publications found

Genes affected

LOC105379243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 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: 0.350 AC: 53225 AN: 151982 Hom.: 9388 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.350 AC: 53241 AN: 152100 Hom.: 9394 Cov.: 33 AF XY: 0.343 AC XY: 25487 AN XY: 74350

African (AFR) AF: 0.332 AC: 13761 AN: 41488

American (AMR) AF: 0.308 AC: 4706 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1464 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1776 AN: 5180

South Asian (SAS) AF: 0.246 AC: 1189 AN: 4828

European-Finnish (FIN) AF: 0.308 AC: 3249 AN: 10556

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25876 AN: 67982

Other (OTH) AF: 0.367 AC: 775 AN: 2114

Alfa AF: 0.369 Hom.: 23402

Bravo AF: 0.350

Asia WGS AF: 0.272 AC: 941 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7001819; hg19: chr8-11650475;