XM_017027568.2:c.11G>A

Variant names:

• chr19-46719053-C-T
• rs929777
• XM_017027568.2:c.11G>A

Variant summary

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

The XM_017027568.2(LOC107987269):​c.11G>A​(p.Gly4Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,998 control chromosomes in the GnomAD database, including 5,492 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (5492 hom., cov: 31)
• Consequence: LOC107987269 XM_017027568.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 6 publications found

Genes affected

LOC107987269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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: 0.267 AC: 40594 AN: 151880 Hom.: 5489 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.267 AC: 40611 AN: 151998 Hom.: 5492 Cov.: 31 AF XY: 0.270 AC XY: 20026 AN XY: 74302

African (AFR) AF: 0.288 AC: 11919 AN: 41432

American (AMR) AF: 0.214 AC: 3268 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3468

East Asian (EAS) AF: 0.108 AC: 558 AN: 5150

South Asian (SAS) AF: 0.199 AC: 958 AN: 4806

European-Finnish (FIN) AF: 0.360 AC: 3824 AN: 10608

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18134 AN: 67936

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.263 Hom.: 9891

Bravo AF: 0.259

Asia WGS AF: 0.160 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.74
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs929777; hg19: chr19-47222310;