chr7-8799087-T-G

Position:

• chr7-8799087-T-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 0.569 in 151,578 control chromosomes in the GnomAD database, including 25,336 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 0.57 (25336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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 = 0.682 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: 0.569 AC: 86134 AN: 151458 Hom.: 25285 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.569 AC: 86243 AN: 151578 Hom.: 25336 Cov.: 31 AF XY: 0.571 AC XY: 42278 AN XY: 74054

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.572

Alfa AF: 0.514 Hom.: 25356

Bravo AF: 0.571

Asia WGS AF: 0.629 AC: 2179 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6463843; hg19: chr7-8838717;