chr5-13603774-A-C

Variant names:

• chr5-13603774-A-C
• rs442392

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 0.709 in 151,992 control chromosomes in the GnomAD database, including 39,500 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 0.71 (39500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107688 AN: 151874 Hom.: 39481 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.709 AC: 107757 AN: 151992 Hom.: 39500 Cov.: 32 AF XY: 0.707 AC XY: 52517 AN XY: 74284

African (AFR) AF: 0.589 AC: 24401 AN: 41422

American (AMR) AF: 0.783 AC: 11949 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2707 AN: 3472

East Asian (EAS) AF: 0.186 AC: 961 AN: 5164

South Asian (SAS) AF: 0.782 AC: 3765 AN: 4816

European-Finnish (FIN) AF: 0.747 AC: 7888 AN: 10562

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53559 AN: 67972

Other (OTH) AF: 0.716 AC: 1511 AN: 2110

Alfa AF: 0.767 Hom.: 186211

Bravo AF: 0.702

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.72
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs442392; hg19: chr5-13603883;