rs428751

Variant names:

• chr5-102129402-T-C
• rs428751

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 0.443 in 152,038 control chromosomes in the GnomAD database, including 15,170 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 0.44 (15170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 6 publications found

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 = 0.466 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: 0.444 AC: 67385 AN: 151920 Hom.: 15163 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.443 AC: 67415 AN: 152038 Hom.: 15170 Cov.: 32 AF XY: 0.441 AC XY: 32769 AN XY: 74330

African (AFR) AF: 0.471 AC: 19537 AN: 41464

American (AMR) AF: 0.391 AC: 5970 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1336 AN: 5174

South Asian (SAS) AF: 0.297 AC: 1431 AN: 4826

European-Finnish (FIN) AF: 0.471 AC: 4970 AN: 10550

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31128 AN: 67962

Other (OTH) AF: 0.441 AC: 931 AN: 2110

Alfa AF: 0.453 Hom.: 43149

Bravo AF: 0.441

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.70
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs428751; hg19: chr5-101465106;