rs6833060

Variant names:

• chr4-4825148-A-G
• rs6833060

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 0.441 in 152,058 control chromosomes in the GnomAD database, including 14,943 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 0.44 (14943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 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: 0.441 AC: 67022 AN: 151940 Hom.: 14923 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.441 AC: 67070 AN: 152058 Hom.: 14943 Cov.: 32 AF XY: 0.438 AC XY: 32524 AN XY: 74326

African (AFR) AF: 0.470 AC: 19460 AN: 41446

American (AMR) AF: 0.357 AC: 5456 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1690 AN: 5162

South Asian (SAS) AF: 0.415 AC: 1997 AN: 4816

European-Finnish (FIN) AF: 0.466 AC: 4931 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30892 AN: 67996

Other (OTH) AF: 0.429 AC: 906 AN: 2110

Alfa AF: 0.445 Hom.: 6672

Bravo AF: 0.429

Asia WGS AF: 0.425 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs6833060; hg19: chr4-4826875;