chr4-29880004-A-T

Position:

• chr4-29880004-A-T

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 0.0801 in 151,920 control chromosomes in the GnomAD database, including 1,235 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 0.080 (1235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0801 AC: 12156 AN: 151802 Hom.: 1236 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.00693

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0801 AC: 12166 AN: 151920 Hom.: 1235 Cov.: 32 AF XY: 0.0801 AC XY: 5950 AN XY: 74252

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0472

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.00692

Gnomad4 OTH AF: 0.0719

Alfa AF: 0.0487 Hom.: 85

Bravo AF: 0.0904

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9291531; hg19: chr4-29881626;