5-91998498-C-T

Variant names:

• chr5-91998498-C-T
• rs7736791

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 0.348 in 151,878 control chromosomes in the GnomAD database, including 13,202 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 0.35 (13202 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.348 AC: 52741 AN: 151758 Hom.: 13155 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.348 AC: 52847 AN: 151878 Hom.: 13202 Cov.: 32 AF XY: 0.347 AC XY: 25748 AN XY: 74216

African (AFR) AF: 0.709 AC: 29377 AN: 41456

American (AMR) AF: 0.275 AC: 4187 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3468

East Asian (EAS) AF: 0.465 AC: 2390 AN: 5144

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1772 AN: 10570

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11981 AN: 67910

Other (OTH) AF: 0.291 AC: 613 AN: 2106

Alfa AF: 0.285 Hom.: 4267

Bravo AF: 0.371

Asia WGS AF: 0.372 AC: 1290 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.25
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7736791; hg19: chr5-91294315;