9-74697774-T-C

Variant names:

• chr9-74697774-T-C
• rs499922

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 0.893 in 152,240 control chromosomes in the GnomAD database, including 60,944 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 0.89 (60944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135867 AN: 152122 Hom.: 60911 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.893 AC: 135956 AN: 152240 Hom.: 60944 Cov.: 32 AF XY: 0.892 AC XY: 66395 AN XY: 74422

African (AFR) AF: 0.827 AC: 34338 AN: 41512

American (AMR) AF: 0.926 AC: 14169 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3052 AN: 3472

East Asian (EAS) AF: 0.806 AC: 4169 AN: 5170

South Asian (SAS) AF: 0.811 AC: 3909 AN: 4820

European-Finnish (FIN) AF: 0.932 AC: 9900 AN: 10620

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63450 AN: 68034

Other (OTH) AF: 0.898 AC: 1896 AN: 2112

Alfa AF: 0.918 Hom.: 106101

Bravo AF: 0.891

Asia WGS AF: 0.830 AC: 2886 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs499922; hg19: chr9-77312690;