XR_001745827.2:n.9752A>G

Variant names:

• chr8-22686645-A-G
• rs1996147
• XR_001745827.2:n.9752A>G

Variant summary

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

The XR_001745827.2(LOC107986924):​n.9752A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,078 control chromosomes in the GnomAD database, including 9,520 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 0.34 (9520 hom., cov: 32)
• Consequence: LOC107986924 XR_001745827.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 13 publications found

Genes affected

LOC107986924 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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: 0.344 AC: 52279 AN: 151960 Hom.: 9508 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.344 AC: 52316 AN: 152078 Hom.: 9520 Cov.: 32 AF XY: 0.349 AC XY: 25944 AN XY: 74340

African (AFR) AF: 0.267 AC: 11053 AN: 41472

American (AMR) AF: 0.430 AC: 6564 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3399 AN: 5166

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4820

European-Finnish (FIN) AF: 0.370 AC: 3912 AN: 10582

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23525 AN: 67968

Other (OTH) AF: 0.329 AC: 695 AN: 2110

Alfa AF: 0.349 Hom.: 9545

Bravo AF: 0.347

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs1996147; hg19: chr8-22544158;