rs6841855

Variant names:

• chr4-57681780-C-T
• rs6841855

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 0.496 in 151,880 control chromosomes in the GnomAD database, including 19,178 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 0.50 (19178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75271 AN: 151758 Hom.: 19164 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.496 AC: 75325 AN: 151880 Hom.: 19178 Cov.: 32 AF XY: 0.502 AC XY: 37236 AN XY: 74220

African (AFR) AF: 0.394 AC: 16312 AN: 41430

American (AMR) AF: 0.570 AC: 8703 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2366 AN: 5146

South Asian (SAS) AF: 0.617 AC: 2958 AN: 4798

European-Finnish (FIN) AF: 0.557 AC: 5865 AN: 10530

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36072 AN: 67928

Other (OTH) AF: 0.490 AC: 1034 AN: 2112

Alfa AF: 0.508 Hom.: 2612

Bravo AF: 0.487

Asia WGS AF: 0.539 AC: 1875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6841855; hg19: chr4-58547946;