rs6683557

Variant names:

• chr1-154879831-C-G
• rs6683557

Your query was ambiguous. Multiple possible variants found:

• chr1-154879831-C-G
• chr1-154879831-C-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 0.526 in 151,882 control chromosomes in the GnomAD database, including 22,322 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 0.53 (22322 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.526 AC: 79855 AN: 151764 Hom.: 22286 Cov.: 30

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.526 AC: 79940 AN: 151882 Hom.: 22322 Cov.: 30 AF XY: 0.532 AC XY: 39456 AN XY: 74212

African (AFR) AF: 0.646 AC: 26750 AN: 41408

American (AMR) AF: 0.589 AC: 8996 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1781 AN: 3470

East Asian (EAS) AF: 0.879 AC: 4544 AN: 5168

South Asian (SAS) AF: 0.626 AC: 3009 AN: 4804

European-Finnish (FIN) AF: 0.419 AC: 4417 AN: 10548

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.426 AC: 28908 AN: 67906

Other (OTH) AF: 0.512 AC: 1079 AN: 2106

Alfa AF: 0.466 Hom.: 2171

Bravo AF: 0.544

Asia WGS AF: 0.747 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs6683557; hg19: chr1-154852307;