rs13427835

chr2-23008130-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124908057 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124908057	XR_007088666.1	n.1947C>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.842 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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.880

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13427835; hg19: chr2-23231002;