1-89306276-A-C

Position:

• chr1-89306276-A-C

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 0.333 in 152,098 control chromosomes in the GnomAD database, including 8,788 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 0.33 (8788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 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: 0.333 AC: 50537 AN: 151980 Hom.: 8771 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.333 AC: 50592 AN: 152098 Hom.: 8788 Cov.: 32 AF XY: 0.339 AC XY: 25221 AN XY: 74344

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.327

Alfa AF: 0.286 Hom.: 3250

Bravo AF: 0.326

Asia WGS AF: 0.518 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2893102; hg19: chr1-89771959;