5-91998498-C-T

Variant names:

• chr5-91998498-C-T
• rs7736791

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 0.348 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.348 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

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.291

Alfa AF: 0.279 Hom.: 2683

Bravo AF: 0.371

Asia WGS AF: 0.372 AC: 1290 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7736791; hg19: chr5-91294315;