rs4098804

chr10-52826568-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 0.198 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;