9-6209697-A-G

Position:

• chr9-6209697-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 0.745 in 151,968 control chromosomes in the GnomAD database, including 42,415 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 0.74 (42415 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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: 0.745 AC: 113078 AN: 151850 Hom.: 42367 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.745 AC: 113188 AN: 151968 Hom.: 42415 Cov.: 30 AF XY: 0.745 AC XY: 55311 AN XY: 74288

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.742

Alfa AF: 0.747 Hom.: 85931

Bravo AF: 0.744

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs992969; hg19: chr9-6209697;