rs13427835

Variant names:

• chr2-23008130-G-C
• rs13427835
• XR_007088666.1:n.1947C>G

Variant summary

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

The XR_007088666.1(LOC124908057):​n.1947C>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 0.842 in 152,136 control chromosomes in the GnomAD database, including 54,952 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 0.84 (54952 hom., cov: 32)
• Consequence: LOC124908057 XR_007088666.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296
• Publications: 1 publications found

Genes affected

LOC124908057 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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: 0.842 AC: 127951 AN: 152016 Hom.: 54925 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.842 AC: 128028 AN: 152136 Hom.: 54952 Cov.: 32 AF XY: 0.841 AC XY: 62578 AN XY: 74376

African (AFR) AF: 0.662 AC: 27442 AN: 41484

American (AMR) AF: 0.893 AC: 13660 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 3312 AN: 3468

East Asian (EAS) AF: 0.833 AC: 4286 AN: 5144

South Asian (SAS) AF: 0.751 AC: 3617 AN: 4814

European-Finnish (FIN) AF: 0.927 AC: 9820 AN: 10596

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62871 AN: 68012

Other (OTH) AF: 0.880 AC: 1861 AN: 2114

Alfa AF: 0.882 Hom.: 7531

Bravo AF: 0.837

Asia WGS AF: 0.799 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.63
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs13427835; hg19: chr2-23231002;