rs7577293

Variant names:

• chr2-85708159-C-T
• rs7577293

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 0.297 in 152,054 control chromosomes in the GnomAD database, including 8,230 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 0.30 (8230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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 (AFR) allele frequency at 95% confidence interval = 0.516 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: 0.297 AC: 45117 AN: 151938 Hom.: 8202 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.297 AC: 45193 AN: 152054 Hom.: 8230 Cov.: 32 AF XY: 0.293 AC XY: 21810 AN XY: 74326

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0495

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.243

Alfa AF: 0.226 Hom.: 6495

Bravo AF: 0.300

Asia WGS AF: 0.191 AC: 663 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	1.3
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7577293; hg19: chr2-85935282;