rs6788877

Variant names:

• chr3-7909448-G-A
• rs6788877

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0588 AC: 2439 AN: 41468

American (AMR) AF: 0.0994 AC: 1518 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.0274 AC: 141 AN: 5140

South Asian (SAS) AF: 0.155 AC: 745 AN: 4816

European-Finnish (FIN) AF: 0.0867 AC: 916 AN: 10566

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8856 AN: 67970

Other (OTH) AF: 0.110 AC: 231 AN: 2106

Alfa AF: 0.116 Hom.: 845

Bravo AF: 0.0997

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.45
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6788877; hg19: chr3-7951135;