chr2-18811761-C-T

Variant names:

• chr2-18811761-C-T
• rs6531119
• XR_001739304.3:n.974-107452C>T

Variant summary

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

The XR_001739304.3(LOC105373456):​n.974-107452C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,906 control chromosomes in the GnomAD database, including 2,757 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 0.17 (2757 hom., cov: 32)
• Consequence: LOC105373456 XR_001739304.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 3 publications found

Genes affected

LOC105373456 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.174 AC: 26479 AN: 151788 Hom.: 2749 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.175 AC: 26508 AN: 151906 Hom.: 2757 Cov.: 32 AF XY: 0.174 AC XY: 12919 AN XY: 74198

African (AFR) AF: 0.0963 AC: 3991 AN: 41448

American (AMR) AF: 0.261 AC: 3980 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3466

East Asian (EAS) AF: 0.411 AC: 2105 AN: 5126

South Asian (SAS) AF: 0.140 AC: 677 AN: 4822

European-Finnish (FIN) AF: 0.131 AC: 1385 AN: 10540

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13101 AN: 67940

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.192 Hom.: 12598

Bravo AF: 0.184

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.53
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6531119; hg19: chr2-18993027;