rs6856768

Variant names:

• chr4-30466544-G-A
• rs6856768

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 0.598 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.427 AC: 17695 AN: 41436

American (AMR) AF: 0.611 AC: 9329 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2258 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1715 AN: 5164

South Asian (SAS) AF: 0.545 AC: 2630 AN: 4828

European-Finnish (FIN) AF: 0.684 AC: 7210 AN: 10538

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47791 AN: 67962

Other (OTH) AF: 0.635 AC: 1336 AN: 2104

Alfa AF: 0.656 Hom.: 82878

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs6856768; hg19: chr4-30468166;