chr8-117217523-C-T

Variant names:

• chr8-117217523-C-T
• rs1995222
• XR_007061067.1:n.560-44035G>A

Variant summary

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

The XR_007061067.1(LOC105375716):​n.560-44035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,870 control chromosomes in the GnomAD database, including 13,937 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 0.42 (13937 hom., cov: 32)
• Consequence: LOC105375716 XR_007061067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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: 0.421 AC: 63918 AN: 151750 Hom.: 13934 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.421 AC: 63955 AN: 151870 Hom.: 13937 Cov.: 32 AF XY: 0.418 AC XY: 31045 AN XY: 74208

African (AFR) AF: 0.340 AC: 14076 AN: 41428

American (AMR) AF: 0.401 AC: 6115 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3466

East Asian (EAS) AF: 0.457 AC: 2361 AN: 5162

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4820

European-Finnish (FIN) AF: 0.528 AC: 5570 AN: 10546

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31951 AN: 67900

Other (OTH) AF: 0.418 AC: 881 AN: 2110

Alfa AF: 0.450 Hom.: 26275

Bravo AF: 0.413

Asia WGS AF: 0.308 AC: 1071 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	0.91
DANN	Benign	0.37
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1995222; hg19: chr8-118229762;