rs7789066

chr7-106287306-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 0.0821 in 152,110 control chromosomes in the GnomAD database, including 573 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 0.082 (573 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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: 0.0820 AC: 12457 AN: 151992 Hom.: 569 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0229

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0821 AC: 12491 AN: 152110 Hom.: 573 Cov.: 33 AF XY: 0.0807 AC XY: 6001 AN XY: 74362

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0943

Alfa AF: 0.0700 Hom.: 865

Bravo AF: 0.0842

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7789066; hg19: chr7-105927752;