rs1002098

Variant names:

• chr4-154927536-C-A
• rs1002098

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 0.239 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.387 AC: 16043 AN: 41496

American (AMR) AF: 0.202 AC: 3091 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3005 AN: 5176

South Asian (SAS) AF: 0.309 AC: 1490 AN: 4820

European-Finnish (FIN) AF: 0.202 AC: 2146 AN: 10598

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9117 AN: 68002

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.168 Hom.: 2217

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1002098; hg19: chr4-155848688;