7-87493531-A-G

Position:

• chr7-87493531-A-G

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 0.293 in 152,086 control chromosomes in the GnomAD database, including 8,719 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 0.29 (8719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763

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 = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44399 AN: 151968 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.293 AC: 44497 AN: 152086 Hom.: 8719 Cov.: 32 AF XY: 0.289 AC XY: 21491 AN XY: 74350

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.259

Alfa AF: 0.208 Hom.: 1894

Bravo AF: 0.308

Asia WGS AF: 0.267 AC: 928 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	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7793196; hg19: chr7-87122847;