rs6670495

Variant names:

• chr1-46722236-T-A
• rs6670495

Your query was ambiguous. Multiple possible variants found:

• chr1-46722236-T-A
• chr1-46722236-T-C
• chr1-46722236-T-G

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 0.409 in 151,872 control chromosomes in the GnomAD database, including 15,229 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 0.41 (15229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62021 AN: 151754 Hom.: 15174 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.409 AC: 62143 AN: 151872 Hom.: 15229 Cov.: 31 AF XY: 0.416 AC XY: 30847 AN XY: 74194

African (AFR) AF: 0.647 AC: 26800 AN: 41390

American (AMR) AF: 0.403 AC: 6159 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3464

East Asian (EAS) AF: 0.800 AC: 4114 AN: 5140

South Asian (SAS) AF: 0.436 AC: 2088 AN: 4794

European-Finnish (FIN) AF: 0.315 AC: 3329 AN: 10578

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17268 AN: 67924

Other (OTH) AF: 0.418 AC: 883 AN: 2110

Alfa AF: 0.322 Hom.: 1152

Bravo AF: 0.428

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.65
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6670495; hg19: chr1-47187908;