rs1881493

Variant names:

• chr2-232489580-C-T
• rs1881493
• XR_007088123.1:n.1282C>T

Variant summary

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

The XR_007088123.1(LOC124906124):​n.1282C>T 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 0.00893 in 152,314 control chromosomes in the GnomAD database, including 44 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 0.0089 (44 hom., cov: 33)
• Consequence: LOC124906124 XR_007088123.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 1 publications found

Genes affected

LOC124906124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906124	XR_007088123.1	n.1282C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304480	ENST00000803679.1	n.953+621C>T		intron_variant	Intron 2 of 3
ENSG00000304480	ENST00000803680.1	n.992+621C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00892 AC: 1358 AN: 152196 Hom.: 45 Cov.: 33

Gnomad AFR AF: 0.00384

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00519

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00209

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.00893 AC: 1360 AN: 152314 Hom.: 44 Cov.: 33 AF XY: 0.0104 AC XY: 774 AN XY: 74464

African (AFR) AF: 0.00387 AC: 161 AN: 41580

American (AMR) AF: 0.0149 AC: 228 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00519 AC: 18 AN: 3470

East Asian (EAS) AF: 0.0927 AC: 478 AN: 5156

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4824

European-Finnish (FIN) AF: 0.0212 AC: 225 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00209 AC: 142 AN: 68034

Other (OTH) AF: 0.0118 AC: 25 AN: 2116

Alfa AF: 0.00572 Hom.: 2

Bravo AF: 0.00806

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs1881493; hg19: chr2-233354290;