rs4841398

chr8-10605296-C-T

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 0.834 in 152,256 control chromosomes in the GnomAD database, including 53,326 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 0.83 (53326 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.861 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: 0.834 AC: 126870 AN: 152138 Hom.: 53298 Cov.: 34

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.834 AC: 126952 AN: 152256 Hom.: 53326 Cov.: 34 AF XY: 0.837 AC XY: 62314 AN XY: 74452

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.832

Alfa AF: 0.855 Hom.: 55668

Bravo AF: 0.823

Asia WGS AF: 0.729 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.0050
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4841398; hg19: chr8-10462806;