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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377842	XR_942658.3	n.431-8325A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;