chr1-159689319-C-T

Variant names:

• chr1-159689319-C-T
• rs12749227

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 0.245 in 152,070 control chromosomes in the GnomAD database, including 5,407 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 0.24 (5407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.245 AC: 37223 AN: 151952 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.245 AC: 37239 AN: 152070 Hom.: 5407 Cov.: 32 AF XY: 0.247 AC XY: 18350 AN XY: 74334

Gnomad4 AFR AF: 0.0975

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0604

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.260

Alfa AF: 0.278 Hom.: 1440

Bravo AF: 0.238

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12749227; hg19: chr1-159659109;