rs6683655

Variant names:

• chr1-188467471-G-A
• rs6683655

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.369 in 151,972 control chromosomes in the GnomAD database, including 10,896 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 0.37 (10896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

ACMG classification

Verdict is Benign. Variant got -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 = 0.425 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: 0.369 AC: 56067 AN: 151854 Hom.: 10876 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.369 AC: 56132 AN: 151972 Hom.: 10896 Cov.: 32 AF XY: 0.369 AC XY: 27404 AN XY: 74274

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.370

Alfa AF: 0.393 Hom.: 1640

Bravo AF: 0.366

Asia WGS AF: 0.217 AC: 757 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6683655; hg19: chr1-188436602;