5-98319582-G-T

Variant names:

• chr5-98319582-G-T
• rs17165849

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.349 in 151,936 control chromosomes in the GnomAD database, including 9,383 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 (9383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.349 AC: 52952 AN: 151820 Hom.: 9379 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.349 AC: 52967 AN: 151936 Hom.: 9383 Cov.: 32 AF XY: 0.352 AC XY: 26138 AN XY: 74214

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.340

Alfa AF: 0.355 Hom.: 5239

Bravo AF: 0.337

Asia WGS AF: 0.360 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	15
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17165849; hg19: chr5-97655286;