rs2893102

Variant names:

• chr1-89306276-A-C
• rs2893102

Your query was ambiguous. Multiple possible variants found:

• chr1-89306276-A-C
• chr1-89306276-A-G
• chr1-89306276-A-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;