rs7589111

Variant names:

• chr2-131413315-G-A
• rs7589111

Your query was ambiguous. Multiple possible variants found:

• chr2-131413315-G-A
• chr2-131413315-G-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 0.523 in 152,038 control chromosomes in the GnomAD database, including 23,566 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 0.52 (23566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.523 AC: 79459 AN: 151922 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.523 AC: 79576 AN: 152038 Hom.: 23566 Cov.: 32 AF XY: 0.528 AC XY: 39213 AN XY: 74306

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.538

Alfa AF: 0.412 Hom.: 15545

Bravo AF: 0.555

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7589111; hg19: chr2-132170888;