XR_942658.3:n.431-8325A>G

Variant names:

• chr6-67319148-A-G
• rs9363741
• XR_942658.3:n.431-8325A>G

Variant summary

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

The XR_942658.3(LOC105377842):​n.431-8325A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,868 control chromosomes in the GnomAD database, including 3,948 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 0.23 (3948 hom., cov: 32)
• Consequence: LOC105377842 XR_942658.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 2 publications found

Genes affected

LOC105377842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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: 0.226 AC: 34252 AN: 151750 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.226 AC: 34272 AN: 151868 Hom.: 3948 Cov.: 32 AF XY: 0.224 AC XY: 16642 AN XY: 74228

African (AFR) AF: 0.157 AC: 6496 AN: 41492

American (AMR) AF: 0.223 AC: 3399 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3468

East Asian (EAS) AF: 0.141 AC: 728 AN: 5164

South Asian (SAS) AF: 0.285 AC: 1375 AN: 4830

European-Finnish (FIN) AF: 0.240 AC: 2529 AN: 10540

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17848 AN: 67810

Other (OTH) AF: 0.236 AC: 497 AN: 2108

Alfa AF: 0.249 Hom.: 21583

Bravo AF: 0.218

Asia WGS AF: 0.211 AC: 732 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.54
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs9363741; hg19: chr6-68029041; COSMIC: COSV69401513;