9-77715802-G-C

Position:

• chr9-77715802-G-C

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 0.83 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.77715802G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.832

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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