rs1446959

chr1-159637014-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;