chr1-159589741-A-G

Variant names:

• chr1-159589741-A-G
• rs1446963

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 0.197 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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

African (AFR) AF: 0.349 AC: 14493 AN: 41482

American (AMR) AF: 0.122 AC: 1867 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3472

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5176

South Asian (SAS) AF: 0.137 AC: 661 AN: 4830

European-Finnish (FIN) AF: 0.173 AC: 1830 AN: 10592

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10108 AN: 68008

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.158 Hom.: 2803

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1446963; hg19: chr1-159559531;