rs6662321

Variant names:

• chr1-46754387-C-T
• rs6662321

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 0.122 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.122 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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0717

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0854

Gnomad4 NFE AF: 0.0613

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0714 Hom.: 703

Bravo AF: 0.124

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6662321; hg19: chr1-47220059;