chr7-27087612-T-C

Variant names:

• chr7-27087612-T-C
• rs2462907

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;