9-6209697-A-G

Variant names:

• chr9-6209697-A-G
• rs992969

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 0.745 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
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.696 AC: 28812 AN: 41410

American (AMR) AF: 0.789 AC: 12044 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2345 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4981 AN: 5182

South Asian (SAS) AF: 0.770 AC: 3702 AN: 4808

European-Finnish (FIN) AF: 0.742 AC: 7840 AN: 10560

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51127 AN: 67970

Other (OTH) AF: 0.742 AC: 1561 AN: 2104

Alfa AF: 0.746 Hom.: 135465

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs992969; hg19: chr9-6209697;