rs6670693

Variant names:

• chr1-1170732-A-G
• rs6670693

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 0.229 in 152,094 control chromosomes in the GnomAD database, including 12,933 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 0.23 (12933 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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: 0.229 AC: 34753 AN: 151978 Hom.: 12890 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.00229

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00605

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.229 AC: 34852 AN: 152094 Hom.: 12933 Cov.: 33 AF XY: 0.222 AC XY: 16512 AN XY: 74346

African (AFR) AF: 0.779 AC: 32358 AN: 41532

American (AMR) AF: 0.105 AC: 1605 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5168

South Asian (SAS) AF: 0.00250 AC: 12 AN: 4808

European-Finnish (FIN) AF: 0.00123 AC: 13 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.00605 AC: 411 AN: 67930

Other (OTH) AF: 0.176 AC: 371 AN: 2110

Alfa AF: 0.127 Hom.: 944

Bravo AF: 0.261

Asia WGS AF: 0.0450 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6670693; hg19: chr1-1106112;