rs4098804

Variant names:

• chr10-52826568-G-A
• rs4098804

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 0.198 in 151,966 control chromosomes in the GnomAD database, including 3,425 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 0.20 (3425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 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: 0.198 AC: 30136 AN: 151850 Hom.: 3420 Cov.: 32

Gnomad AFR AF: 0.0996

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.198 AC: 30145 AN: 151966 Hom.: 3425 Cov.: 32 AF XY: 0.200 AC XY: 14874 AN XY: 74224

Gnomad4 AFR AF: 0.0995

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.210

Alfa AF: 0.224 Hom.: 681

Bravo AF: 0.204

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4098804; hg19: chr10-54586328;