4-98874173-G-A

Position:

• chr4-98874173-G-A

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 0.455 in 151,918 control chromosomes in the GnomAD database, including 17,061 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 0.45 (17061 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68959 AN: 151804 Hom.: 17027 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.461

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.455 AC: 69058 AN: 151918 Hom.: 17061 Cov.: 32 AF XY: 0.446 AC XY: 33112 AN XY: 74228

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.460

Alfa AF: 0.339 Hom.: 1588

Bravo AF: 0.469

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332467; hg19: chr4-99795324;