chr2-23008130-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124908057	XR_007088666.1	n.1947C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;