rs4841398

Variant names:

• chr8-10605296-C-T
• rs4841398

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 0.834 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.782 AC: 32475 AN: 41506

American (AMR) AF: 0.821 AC: 12558 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3001 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3009 AN: 5178

South Asian (SAS) AF: 0.883 AC: 4267 AN: 4830

European-Finnish (FIN) AF: 0.934 AC: 9908 AN: 10610

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.867 AC: 58969 AN: 68040

Other (OTH) AF: 0.832 AC: 1759 AN: 2114

Alfa AF: 0.848 Hom.: 153750

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
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs4841398; hg19: chr8-10462806;