5-98319582-G-T

Variant names:

• chr5-98319582-G-T
• rs17165849

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.301 AC: 12480 AN: 41462

American (AMR) AF: 0.352 AC: 5368 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1168 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2097 AN: 5148

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4810

European-Finnish (FIN) AF: 0.432 AC: 4559 AN: 10542

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24447 AN: 67954

Other (OTH) AF: 0.340 AC: 717 AN: 2110

Alfa AF: 0.352 Hom.: 7218

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
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs17165849; hg19: chr5-97655286;