9-71584897-T-C

Variant names:

• chr9-71584897-T-C
• rs9314788

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 0.939 in 152,268 control chromosomes in the GnomAD database, including 67,223 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 0.94 (67223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.977 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: 0.939 AC: 142905 AN: 152150 Hom.: 67169 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.939 AC: 143018 AN: 152268 Hom.: 67223 Cov.: 32 AF XY: 0.941 AC XY: 70091 AN XY: 74452

African (AFR) AF: 0.917 AC: 38100 AN: 41534

American (AMR) AF: 0.957 AC: 14650 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3250 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5179 AN: 5180

South Asian (SAS) AF: 0.980 AC: 4728 AN: 4826

European-Finnish (FIN) AF: 0.947 AC: 10049 AN: 10608

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63955 AN: 68024

Other (OTH) AF: 0.952 AC: 2013 AN: 2114

Alfa AF: 0.939 Hom.: 112309

Bravo AF: 0.938

Asia WGS AF: 0.987 AC: 3432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.33
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9314788; hg19: chr9-74199813;