rs2462907

chr7-27087612-T-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 0.487 in 151,866 control chromosomes in the GnomAD database, including 18,218 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 0.49 (18218 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73972 AN: 151748 Hom.: 18205 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.487 AC: 74033 AN: 151866 Hom.: 18218 Cov.: 31 AF XY: 0.482 AC XY: 35750 AN XY: 74186

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.494

Alfa AF: 0.492 Hom.: 10835

Bravo AF: 0.492

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.4
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2462907; hg19: chr7-27127231;