5-32804422-T-C

Variant names:

• chr5-32804422-T-C
• rs1173766

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.603 AC: 24962 AN: 41414

American (AMR) AF: 0.556 AC: 8486 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2026 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3364 AN: 5166

South Asian (SAS) AF: 0.581 AC: 2802 AN: 4824

European-Finnish (FIN) AF: 0.567 AC: 5960 AN: 10512

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37720 AN: 67934

Other (OTH) AF: 0.580 AC: 1220 AN: 2102

Alfa AF: 0.564 Hom.: 28811

Bravo AF: 0.573

Asia WGS AF: 0.611 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.12
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1173766; hg19: chr5-32804528;