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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986924	XR_001745827.2	n.9752A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

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

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 v4.3

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;