rs6841855

Variant names:

• chr4-57681780-C-T
• rs6841855

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 0.496 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.496 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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.490

Alfa AF: 0.514 Hom.: 2552

Bravo AF: 0.487

Asia WGS AF: 0.539 AC: 1875 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6841855; hg19: chr4-58547946;