XR_007063754.1:n.2886A>G

Variant names:

• chr13-34080781-A-G
• rs690705
• XR_007063754.1:n.2886A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

LOC124903153 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.246 AC: 10194 AN: 41480

American (AMR) AF: 0.389 AC: 5932 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1360 AN: 5180

South Asian (SAS) AF: 0.261 AC: 1255 AN: 4814

European-Finnish (FIN) AF: 0.336 AC: 3546 AN: 10552

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20926 AN: 67970

Other (OTH) AF: 0.286 AC: 605 AN: 2116

Alfa AF: 0.304 Hom.: 33731

Bravo AF: 0.299

Asia WGS AF: 0.247 AC: 859 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.015
DANN	Benign	0.47
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs690705; hg19: chr13-34654918;