5-32804422-T-C

Variant names:

• chr5-32804422-T-C
• rs1173766

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;