rs6668659

Variant names:

• chr1-11862241-T-G
• rs6668659

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 0.338 in 151,968 control chromosomes in the GnomAD database, including 8,941 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 0.34 (8941 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.39 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: 0.338 AC: 51250 AN: 151852 Hom.: 8916 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.338 AC: 51314 AN: 151968 Hom.: 8941 Cov.: 31 AF XY: 0.334 AC XY: 24829 AN XY: 74278

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.340

Alfa AF: 0.338 Hom.: 8642

Bravo AF: 0.333

Asia WGS AF: 0.326 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.055
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6668659; hg19: chr1-11922298; COSMIC: COSV64687439;