5-40437846-C-T

Variant names:

• chr5-40437846-C-T
• rs9292777

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 0.588 in 151,928 control chromosomes in the GnomAD database, including 27,156 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 0.59 (27156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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: 0.588 AC: 89250 AN: 151810 Hom.: 27142 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.588 AC: 89311 AN: 151928 Hom.: 27156 Cov.: 31 AF XY: 0.579 AC XY: 43017 AN XY: 74250

African (AFR) AF: 0.675 AC: 27952 AN: 41410

American (AMR) AF: 0.485 AC: 7412 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2146 AN: 3468

East Asian (EAS) AF: 0.137 AC: 709 AN: 5172

South Asian (SAS) AF: 0.467 AC: 2250 AN: 4820

European-Finnish (FIN) AF: 0.543 AC: 5713 AN: 10512

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41144 AN: 67964

Other (OTH) AF: 0.595 AC: 1249 AN: 2098

Alfa AF: 0.594 Hom.: 107630

Bravo AF: 0.584

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9292777; hg19: chr5-40437948;