9-77705449-A-G

Variant names:

• chr9-77705449-A-G
• rs4745661

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 0.645 in 151,944 control chromosomes in the GnomAD database, including 32,309 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 0.64 (32309 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.714 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: 0.645 AC: 97951 AN: 151826 Hom.: 32300 Cov.: 30

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.645 AC: 97999 AN: 151944 Hom.: 32309 Cov.: 30 AF XY: 0.642 AC XY: 47668 AN XY: 74260

African (AFR) AF: 0.529 AC: 21922 AN: 41426

American (AMR) AF: 0.657 AC: 10043 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2328 AN: 5138

South Asian (SAS) AF: 0.627 AC: 3017 AN: 4810

European-Finnish (FIN) AF: 0.686 AC: 7243 AN: 10566

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48843 AN: 67946

Other (OTH) AF: 0.657 AC: 1385 AN: 2108

Alfa AF: 0.679 Hom.: 49210

Bravo AF: 0.636

Asia WGS AF: 0.590 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.59
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs4745661; hg19: chr9-80320365;