XR_929042.3:n.798-6401T>C

Variant names:

• chr8-72523859-A-G
• rs12550268
• XR_929042.3:n.798-6401T>C

Variant summary

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

The XR_929042.3(LOC105375897):​n.798-6401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,140 control chromosomes in the GnomAD database, including 17,410 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 0.43 (17410 hom., cov: 32)
• Consequence: LOC105375897 XR_929042.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 3 publications found

Genes affected

LOC105375897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65436 AN: 152022 Hom.: 17398 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.430 AC: 65469 AN: 152140 Hom.: 17410 Cov.: 32 AF XY: 0.432 AC XY: 32126 AN XY: 74370

African (AFR) AF: 0.123 AC: 5113 AN: 41542

American (AMR) AF: 0.575 AC: 8778 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1105 AN: 5186

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4814

European-Finnish (FIN) AF: 0.594 AC: 6291 AN: 10586

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39052 AN: 67966

Other (OTH) AF: 0.433 AC: 915 AN: 2112

Alfa AF: 0.501 Hom.: 39429

Bravo AF: 0.419

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.57
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs12550268; hg19: chr8-73436094;