rs6856768

Positions:

• chr4-30466544-G-A

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 0.598 in 151,986 control chromosomes in the GnomAD database, including 28,455 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 0.60 (28455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90822 AN: 151868 Hom.: 28440 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.598 AC: 90861 AN: 151986 Hom.: 28455 Cov.: 32 AF XY: 0.595 AC XY: 44219 AN XY: 74284

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.635

Alfa AF: 0.666 Hom.: 14973

Bravo AF: 0.584

Asia WGS AF: 0.450 AC: 1567 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6856768; hg19: chr4-30468166;