rs7789754

chr7-53980332-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 0.1 in 152,186 control chromosomes in the GnomAD database, including 812 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 0.10 (812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.100 AC: 15209 AN: 152068 Hom.: 813 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.100 AC: 15222 AN: 152186 Hom.: 812 Cov.: 32 AF XY: 0.102 AC XY: 7619 AN XY: 74414

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0985

Alfa AF: 0.0961 Hom.: 756

Bravo AF: 0.0963

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7789754; hg19: chr7-54048025;