rs6662321

Variant names:

• chr1-46754387-C-T
• rs6662321

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 0.122 in 152,106 control chromosomes in the GnomAD database, including 1,782 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 0.12 (1782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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: 0.122 AC: 18501 AN: 151988 Hom.: 1766 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0717

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.122 AC: 18553 AN: 152106 Hom.: 1782 Cov.: 32 AF XY: 0.122 AC XY: 9110 AN XY: 74372

African (AFR) AF: 0.270 AC: 11187 AN: 41466

American (AMR) AF: 0.0674 AC: 1031 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0717 AC: 249 AN: 3472

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5186

South Asian (SAS) AF: 0.139 AC: 669 AN: 4818

European-Finnish (FIN) AF: 0.0854 AC: 903 AN: 10576

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0613 AC: 4167 AN: 67978

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.0766 Hom.: 1114

Bravo AF: 0.124

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.73
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6662321; hg19: chr1-47220059;