chr4-29901430-G-A

Position:

• chr4-29901430-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.32 in 151,978 control chromosomes in the GnomAD database, including 8,419 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 0.32 (8419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48505 AN: 151860 Hom.: 8397 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.320 AC: 48570 AN: 151978 Hom.: 8419 Cov.: 32 AF XY: 0.314 AC XY: 23302 AN XY: 74288

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.313

Alfa AF: 0.278 Hom.: 11565

Bravo AF: 0.326

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7442317; hg19: chr4-29903052;