9-77168868-T-G

Position:

• chr9-77168868-T-G

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 0.491 in 152,078 control chromosomes in the GnomAD database, including 18,829 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 0.49 (18829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74625 AN: 151960 Hom.: 18819 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.491 AC: 74667 AN: 152078 Hom.: 18829 Cov.: 32 AF XY: 0.494 AC XY: 36721 AN XY: 74344

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.519

Alfa AF: 0.496 Hom.: 7951

Bravo AF: 0.492

Asia WGS AF: 0.574 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12156507; hg19: chr9-79783784;