5-98319582-G-T

Position:

• chr5-98319582-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;