5-32804422-T-C

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 0.574 in 151,884 control chromosomes in the GnomAD database, including 25,302 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 0.57 (25302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87152 AN: 151766 Hom.: 25272 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.574 AC: 87237 AN: 151884 Hom.: 25302 Cov.: 31 AF XY: 0.575 AC XY: 42661 AN XY: 74228

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.580

Alfa AF: 0.561 Hom.: 2992

Bravo AF: 0.573

Asia WGS AF: 0.611 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1173766; hg19: chr5-32804528;