rs13272392

Positions:

• chr8-23670998-T-A
• chr8-23670998-T-C
• chr8-23670998-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745842.2(LOC107986930):​n.1312+2248T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,048 control chromosomes in the GnomAD database, including 20,331 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 0.51 (20331 hom., cov: 32)
• Consequence: LOC107986930 XR_001745842.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

LOC107986930 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986930	XR_001745842.2	n.1312+2248T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76794 AN: 151930 Hom.: 20328 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.505 AC: 76821 AN: 152048 Hom.: 20331 Cov.: 32 AF XY: 0.505 AC XY: 37496 AN XY: 74318

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.509

Alfa AF: 0.524 Hom.: 2607

Bravo AF: 0.504

Asia WGS AF: 0.561 AC: 1944 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	16
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13272392; hg19: chr8-23528511; COSMIC: COSV70618196;