rs6663083

Variant names:

• chr1-197011530-T-C
• rs6663083

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 0.383 in 151,968 control chromosomes in the GnomAD database, including 12,796 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 0.38 (12796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 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: 0.383 AC: 58220 AN: 151850 Hom.: 12786 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.383 AC: 58239 AN: 151968 Hom.: 12796 Cov.: 32 AF XY: 0.377 AC XY: 28026 AN XY: 74278

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.389

Alfa AF: 0.445 Hom.: 5709

Bravo AF: 0.366

Asia WGS AF: 0.259 AC: 902 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
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: rs6663083; hg19: chr1-196980660;