rs929777

Positions:

• chr19-46719053-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107987269 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987269	XM_017027568.2	c.11G>A	p.Gly4Glu	missense_variant	1/4		XP_016883057.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.267

Alfa AF: 0.266 Hom.: 7207

Bravo AF: 0.259

Asia WGS AF: 0.160 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs929777; hg19: chr19-47222310;