9-74282154-A-G

Position:

• chr9-74282154-A-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 0.639 in 151,972 control chromosomes in the GnomAD database, including 34,104 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 (34104 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97106 AN: 151854 Hom.: 34089 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.639 AC: 97152 AN: 151972 Hom.: 34104 Cov.: 31 AF XY: 0.648 AC XY: 48128 AN XY: 74290

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.692

Alfa AF: 0.636 Hom.: 4774

Bravo AF: 0.624

Asia WGS AF: 0.864 AC: 3004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4013967; hg19: chr9-76897070;