chr1-189908801-G-A

Position:

• chr1-189908801-G-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 0.273 in 151,934 control chromosomes in the GnomAD database, including 6,160 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 0.27 (6160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.273 AC: 41494 AN: 151818 Hom.: 6150 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.273 AC: 41525 AN: 151934 Hom.: 6160 Cov.: 32 AF XY: 0.272 AC XY: 20166 AN XY: 74236

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.259

Alfa AF: 0.257 Hom.: 1037

Bravo AF: 0.274

Asia WGS AF: 0.232 AC: 798 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341974; hg19: chr1-189877931;