rs7789754

Variant names:

• chr7-53980332-A-G
• rs7789754

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;