rs690705

chr13-34080781-A-G

Variant summary

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

The XR_007063754.1(LOC124903153):n.2886A>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 0.296 in 152,054 control chromosomes in the GnomAD database, including 6,863 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 0.30 (6863 hom., cov: 32)
• Consequence: LOC124903153 XR_007063754.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

Genes affected

LOC124903153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903153	XR_007063754.1	n.2886A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44949 AN: 151936 Hom.: 6863 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.296 AC: 44966 AN: 152054 Hom.: 6863 Cov.: 32 AF XY: 0.299 AC XY: 22203 AN XY: 74312

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.286

Alfa AF: 0.302 Hom.: 16038

Bravo AF: 0.299

Asia WGS AF: 0.247 AC: 859 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.015
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs690705; hg19: chr13-34654918;