chr8-117208031-T-C

Variant names:

• chr8-117208031-T-C
• rs11774700
• XR_007061067.1:n.560-34543A>G

Variant summary

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

The XR_928568.4(LOC105375716):​n.715-34543A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,104 control chromosomes in the GnomAD database, including 5,897 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 0.26 (5897 hom., cov: 33)
• Consequence: LOC105375716 XR_928568.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 16 publications found

Genes affected

LOC105375716 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.259 AC: 39423 AN: 151986 Hom.: 5895 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.259 AC: 39436 AN: 152104 Hom.: 5897 Cov.: 33 AF XY: 0.265 AC XY: 19705 AN XY: 74350

African (AFR) AF: 0.123 AC: 5111 AN: 41526

American (AMR) AF: 0.257 AC: 3926 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2369 AN: 5150

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4826

European-Finnish (FIN) AF: 0.411 AC: 4346 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20721 AN: 67968

Other (OTH) AF: 0.263 AC: 557 AN: 2116

Alfa AF: 0.289 Hom.: 9368

Bravo AF: 0.247

Asia WGS AF: 0.302 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11774700; hg19: chr8-118220270;