XR_949569.4:n.72-8463T>C

Variant names:

• chr8-20781983-T-C
• rs10089021
• XR_949569.4:n.72-8463T>C

Variant summary

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

The XR_949569.4(LOC105379315):​n.72-8463T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,892 control chromosomes in the GnomAD database, including 4,115 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 (4115 hom., cov: 32)
• Consequence: LOC105379315 XR_949569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

Genes affected

LOC105379315 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.349 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: 0.229 AC: 34817 AN: 151774 Hom.: 4104 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.229 AC: 34854 AN: 151892 Hom.: 4115 Cov.: 32 AF XY: 0.228 AC XY: 16943 AN XY: 74236

African (AFR) AF: 0.198 AC: 8182 AN: 41420

American (AMR) AF: 0.231 AC: 3531 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3464

East Asian (EAS) AF: 0.342 AC: 1755 AN: 5126

South Asian (SAS) AF: 0.363 AC: 1746 AN: 4804

European-Finnish (FIN) AF: 0.183 AC: 1932 AN: 10574

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.235 AC: 15957 AN: 67928

Other (OTH) AF: 0.247 AC: 521 AN: 2108

Alfa AF: 0.240 Hom.: 2718

Bravo AF: 0.230

Asia WGS AF: 0.367 AC: 1276 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	4.6
DANN	Benign	0.48
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs10089021; hg19: chr8-20639494;