rs6788877

Variant names:

• chr3-7909448-G-A
• rs6788877

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;