rs1446963

Positions:

• chr1-159589741-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;