4-32296333-C-T

Variant names:

• chr4-32296333-C-T
• rs7655505

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;