5-98420678-T-G

Variant names:

• chr5-98420678-T-G
• rs1455420

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 0.342 in 151,904 control chromosomes in the GnomAD database, including 9,639 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 0.34 (9639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.342 AC: 51889 AN: 151786 Hom.: 9635 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.342 AC: 51902 AN: 151904 Hom.: 9639 Cov.: 32 AF XY: 0.346 AC XY: 25691 AN XY: 74220

African (AFR) AF: 0.193 AC: 7992 AN: 41498

American (AMR) AF: 0.380 AC: 5788 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2599 AN: 5156

South Asian (SAS) AF: 0.373 AC: 1798 AN: 4816

European-Finnish (FIN) AF: 0.458 AC: 4821 AN: 10516

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26330 AN: 67906

Other (OTH) AF: 0.368 AC: 779 AN: 2114

Alfa AF: 0.345 Hom.: 4746

Bravo AF: 0.328

Asia WGS AF: 0.398 AC: 1382 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.68
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1455420;

hg19: chr5-97756382;