rs1002098

Positions:

• chr4-154927536-C-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 0.239 in 152,176 control chromosomes in the GnomAD database, including 5,632 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 0.24 (5632 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

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 (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.239 AC: 36335 AN: 152058 Hom.: 5628 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.239 AC: 36366 AN: 152176 Hom.: 5632 Cov.: 33 AF XY: 0.245 AC XY: 18193 AN XY: 74406

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.245

Alfa AF: 0.167 Hom.: 1873

Bravo AF: 0.244

Asia WGS AF: 0.413 AC: 1432 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	0.33
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002098; hg19: chr4-155848688;