rs6683580

Variant names:

• chr1-161714779-A-G
• rs6683580

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 0.437 in 151,988 control chromosomes in the GnomAD database, including 18,465 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 0.44 (18465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 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: 0.436 AC: 66284 AN: 151868 Hom.: 18413 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.437 AC: 66391 AN: 151988 Hom.: 18465 Cov.: 32 AF XY: 0.435 AC XY: 32329 AN XY: 74300

African (AFR) AF: 0.776 AC: 32175 AN: 41452

American (AMR) AF: 0.437 AC: 6672 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3321 AN: 5168

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4820

European-Finnish (FIN) AF: 0.251 AC: 2645 AN: 10558

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17755 AN: 67946

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.319 Hom.: 15780

Bravo AF: 0.471

Asia WGS AF: 0.508 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.46
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6683580; hg19: chr1-161684569;