rs6827820

Variant names:

• chr4-82467738-C-T
• rs6827820

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 0.547 in 152,048 control chromosomes in the GnomAD database, including 22,981 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 0.55 (22981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) 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: 0.547 AC: 83038 AN: 151930 Hom.: 22952 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.547 AC: 83115 AN: 152048 Hom.: 22981 Cov.: 32 AF XY: 0.554 AC XY: 41158 AN XY: 74330

African (AFR) AF: 0.536 AC: 22242 AN: 41464

American (AMR) AF: 0.654 AC: 9984 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1667 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2693 AN: 5154

South Asian (SAS) AF: 0.659 AC: 3171 AN: 4814

European-Finnish (FIN) AF: 0.593 AC: 6274 AN: 10582

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35238 AN: 67980

Other (OTH) AF: 0.540 AC: 1139 AN: 2108

Alfa AF: 0.531 Hom.: 12396

Bravo AF: 0.547

Asia WGS AF: 0.583 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.45
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6827820; hg19: chr4-83388891;