rs6858086

Variant names:

• chr4-73871754-T-C
• rs6858086

Your query was ambiguous. Multiple possible variants found:

• chr4-73871754-T-C
• chr4-73871754-T-G

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 0.469 in 152,088 control chromosomes in the GnomAD database, including 20,769 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 0.47 (20769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 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: 0.470 AC: 71361 AN: 151970 Hom.: 20775 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.469 AC: 71343 AN: 152088 Hom.: 20769 Cov.: 32 AF XY: 0.468 AC XY: 34823 AN XY: 74342

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.475

Alfa AF: 0.547 Hom.: 4341

Bravo AF: 0.440

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.95
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6858086; hg19: chr4-74737471;