rs1446963

Variant names:

• chr1-159589741-A-G
• rs1446963

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 0.197 in 152,182 control chromosomes in the GnomAD database, including 3,761 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 0.20 (3761 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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: 0.196 AC: 29878 AN: 152064 Hom.: 3747 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.197 AC: 29935 AN: 152182 Hom.: 3761 Cov.: 33 AF XY: 0.196 AC XY: 14598 AN XY: 74420

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.173

Alfa AF: 0.150 Hom.: 1839

Bravo AF: 0.197

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.069
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446963; hg19: chr1-159559531;