9-77161416-A-G

Variant names:

• chr9-77161416-A-G
• rs10512064

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 0.112 in 152,210 control chromosomes in the GnomAD database, including 990 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 0.11 (990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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: 0.112 AC: 16960 AN: 152092 Hom.: 986 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.112 AC: 16978 AN: 152210 Hom.: 990 Cov.: 32 AF XY: 0.110 AC XY: 8189 AN XY: 74428

African (AFR) AF: 0.114 AC: 4738 AN: 41536

American (AMR) AF: 0.0845 AC: 1292 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.0369 AC: 191 AN: 5180

South Asian (SAS) AF: 0.0961 AC: 464 AN: 4828

European-Finnish (FIN) AF: 0.126 AC: 1340 AN: 10598

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8225 AN: 67988

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.115 Hom.: 1744

Bravo AF: 0.108

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.72
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10512064; hg19: chr9-79776332;