9-77715802-G-C

Variant names:

• chr9-77715802-G-C
• rs4745664

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 0.83 in 152,120 control chromosomes in the GnomAD database, including 52,918 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 0.83 (52918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.830 AC: 126172 AN: 152002 Hom.: 52863 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.830 AC: 126286 AN: 152120 Hom.: 52918 Cov.: 31 AF XY: 0.831 AC XY: 61801 AN XY: 74364

African (AFR) AF: 0.937 AC: 38893 AN: 41518

American (AMR) AF: 0.871 AC: 13316 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2799 AN: 3472

East Asian (EAS) AF: 0.777 AC: 3999 AN: 5148

South Asian (SAS) AF: 0.808 AC: 3892 AN: 4814

European-Finnish (FIN) AF: 0.795 AC: 8411 AN: 10576

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52202 AN: 67992

Other (OTH) AF: 0.832 AC: 1755 AN: 2110

Alfa AF: 0.791 Hom.: 5983

Bravo AF: 0.840

Asia WGS AF: 0.849 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4745664; hg19: chr9-80330718; COSMIC: COSV54108371;