chr4-32296333-C-T

Position:

• chr4-32296333-C-T

Variant summary

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

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 0.43 (4378 hom., cov: 14)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 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: 0.425 AC: 33747 AN: 79340 Hom.: 4379 Cov.: 14

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.444

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.425 AC: 33744 AN: 79338 Hom.: 4378 Cov.: 14 AF XY: 0.420 AC XY: 16148 AN XY: 38416

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.88
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7655505; hg19: chr4-32297955;