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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.375 AC: 15542 AN: 41486

American (AMR) AF: 0.297 AC: 4532 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2681 AN: 5162

South Asian (SAS) AF: 0.530 AC: 2556 AN: 4824

European-Finnish (FIN) AF: 0.332 AC: 3510 AN: 10586

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19573 AN: 67976

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.288 Hom.: 3653

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2893102; hg19: chr1-89771959;