rs1446959

Variant names:

• chr1-159637014-T-A
• rs1446959

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 0.549 in 151,932 control chromosomes in the GnomAD database, including 26,035 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 0.55 (26035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.549 AC: 83273 AN: 151814 Hom.: 25992 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.549 AC: 83380 AN: 151932 Hom.: 26035 Cov.: 32 AF XY: 0.544 AC XY: 40418 AN XY: 74280

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.0863

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.530

Alfa AF: 0.515 Hom.: 2740

Bravo AF: 0.563

Asia WGS AF: 0.256 AC: 893 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446959; hg19: chr1-159606804;