rs6427809

Variant names:

• chr1-200220293-A-G
• rs6427809

Your query was ambiguous. Multiple possible variants found:

• chr1-200220293-A-G
• chr1-200220293-A-T

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 0.617 in 151,936 control chromosomes in the GnomAD database, including 29,442 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 0.62 (29442 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 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: 0.617 AC: 93641 AN: 151818 Hom.: 29422 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.617 AC: 93695 AN: 151936 Hom.: 29442 Cov.: 31 AF XY: 0.616 AC XY: 45753 AN XY: 74236

African (AFR) AF: 0.529 AC: 21906 AN: 41408

American (AMR) AF: 0.584 AC: 8905 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2078 AN: 3472

East Asian (EAS) AF: 0.510 AC: 2630 AN: 5154

South Asian (SAS) AF: 0.663 AC: 3191 AN: 4816

European-Finnish (FIN) AF: 0.710 AC: 7494 AN: 10558

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45337 AN: 67962

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.628 Hom.: 4605

Bravo AF: 0.604

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6427809; hg19: chr1-200189421;