7-87067398-A-G

Position:

• chr7-87067398-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.128 in 152,136 control chromosomes in the GnomAD database, including 1,375 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 0.13 (1375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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: 0.128 AC: 19412 AN: 152018 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.128 AC: 19448 AN: 152136 Hom.: 1375 Cov.: 32 AF XY: 0.130 AC XY: 9677 AN XY: 74386

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.112

Alfa AF: 0.118 Hom.: 1015

Bravo AF: 0.128

Asia WGS AF: 0.253 AC: 874 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	8.8
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476587; hg19: chr7-86696714;