rs6679047

Variant names:

• chr1-199646570-C-T
• rs6679047

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 0.081 in 152,256 control chromosomes in the GnomAD database, including 695 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 0.081 (695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0810 AC: 12329 AN: 152138 Hom.: 696 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0810 AC: 12338 AN: 152256 Hom.: 695 Cov.: 32 AF XY: 0.0798 AC XY: 5938 AN XY: 74456

African (AFR) AF: 0.140 AC: 5801 AN: 41526

American (AMR) AF: 0.127 AC: 1940 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.121 AC: 628 AN: 5188

South Asian (SAS) AF: 0.0366 AC: 177 AN: 4830

European-Finnish (FIN) AF: 0.0191 AC: 203 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3297 AN: 68016

Other (OTH) AF: 0.0818 AC: 173 AN: 2116

Alfa AF: 0.0593 Hom.: 222

Bravo AF: 0.0948

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.43
PhyloP100		1.3

Splicing

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

Publications

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Other links and lift over

dbSNP: rs6679047; hg19: chr1-199615698;