2-18766049-G-A

Variant names:

• chr2-18766049-G-A
• rs11885014
• XR_001739304.3:n.973+77721G>A

Variant summary

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

The XR_001739304.3(LOC105373456):​n.973+77721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,872 control chromosomes in the GnomAD database, including 10,229 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 0.34 (10229 hom., cov: 32)
• Consequence: LOC105373456 XR_001739304.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.337 AC: 51161 AN: 151754 Hom.: 10199 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.337 AC: 51233 AN: 151872 Hom.: 10229 Cov.: 32 AF XY: 0.331 AC XY: 24588 AN XY: 74226

African (AFR) AF: 0.546 AC: 22616 AN: 41418

American (AMR) AF: 0.278 AC: 4234 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3466

East Asian (EAS) AF: 0.0808 AC: 417 AN: 5164

South Asian (SAS) AF: 0.155 AC: 743 AN: 4806

European-Finnish (FIN) AF: 0.260 AC: 2748 AN: 10552

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18499 AN: 67926

Other (OTH) AF: 0.302 AC: 635 AN: 2106

Alfa AF: 0.267 Hom.: 8133

Bravo AF: 0.348

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11885014; hg19: chr2-18947315;