rs929819

Variant names:

• chr5-51719663-C-T
• rs929819

Variant summary

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

The variant allele was found at a frequency of 0.355 in 151,976 control chromosomes in the GnomAD database, including 10,023 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 0.36 (10023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53952 AN: 151858 Hom.: 10016 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.355 AC: 53969 AN: 151976 Hom.: 10023 Cov.: 32 AF XY: 0.352 AC XY: 26174 AN XY: 74268

African (AFR) AF: 0.347 AC: 14397 AN: 41436

American (AMR) AF: 0.345 AC: 5268 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.0683 AC: 353 AN: 5170

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4826

European-Finnish (FIN) AF: 0.403 AC: 4244 AN: 10542

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26149 AN: 67960

Other (OTH) AF: 0.331 AC: 695 AN: 2102

Alfa AF: 0.371 Hom.: 1320

Bravo AF: 0.350

Asia WGS AF: 0.174 AC: 603 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs929819; hg19: chr5-51015497;