9-136932121-T-G

Variant names:

• chr9-136932121-T-G
• rs4880166

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 0.78 in 152,034 control chromosomes in the GnomAD database, including 46,727 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 0.78 (46727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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: 0.780 AC: 118547 AN: 151916 Hom.: 46688 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.780 AC: 118645 AN: 152034 Hom.: 46727 Cov.: 32 AF XY: 0.780 AC XY: 57980 AN XY: 74318

African (AFR) AF: 0.883 AC: 36601 AN: 41472

American (AMR) AF: 0.651 AC: 9940 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2611 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4491 AN: 5170

South Asian (SAS) AF: 0.797 AC: 3841 AN: 4818

European-Finnish (FIN) AF: 0.755 AC: 7956 AN: 10536

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50669 AN: 67990

Other (OTH) AF: 0.758 AC: 1600 AN: 2112

Alfa AF: 0.785 Hom.: 6730

Bravo AF: 0.775

Asia WGS AF: 0.809 AC: 2811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4880166; hg19: chr9-139826573;