1-89100413-G-A

Position:

• chr1-89100413-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 0.398 in 151,770 control chromosomes in the GnomAD database, including 13,487 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 0.40 (13487 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.398 AC: 60382 AN: 151652 Hom.: 13490 Cov.: 29

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.398 AC: 60372 AN: 151770 Hom.: 13487 Cov.: 29 AF XY: 0.402 AC XY: 29831 AN XY: 74178

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.405

Alfa AF: 0.458 Hom.: 2133

Bravo AF: 0.366

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12725861; hg19: chr1-89566096; COSMIC: COSV71575918;