rs6841855

Positions:

• chr4-57681780-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 0.496 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;