rs6788877

chr3-7909448-G-A

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 0.102 in 152,014 control chromosomes in the GnomAD database, including 930 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 (930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.102 AC: 15446 AN: 151896 Hom.: 929 Cov.: 31

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.102 AC: 15459 AN: 152014 Hom.: 930 Cov.: 31 AF XY: 0.0995 AC XY: 7390 AN XY: 74272

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0274

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.110

Alfa AF: 0.119 Hom.: 636

Bravo AF: 0.0997

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.18
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6788877; hg19: chr3-7951135;