rs7584099

Variant names:

• chr2-147720767-A-G
• rs7584099

Your query was ambiguous. Multiple possible variants found:

• chr2-147720767-A-G
• chr2-147720767-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 0.42 in 151,990 control chromosomes in the GnomAD database, including 14,249 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 0.42 (14249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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: 0.420 AC: 63845 AN: 151872 Hom.: 14230 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.420 AC: 63905 AN: 151990 Hom.: 14249 Cov.: 32 AF XY: 0.431 AC XY: 31991 AN XY: 74286

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.417

Alfa AF: 0.441 Hom.: 22598

Bravo AF: 0.414

Asia WGS AF: 0.554 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7584099; hg19: chr2-148478336;