chr9-136563054-C-T

Variant names:

• chr9-136563054-C-T
• rs7849014

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 0.867 in 152,256 control chromosomes in the GnomAD database, including 57,761 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 0.87 (57761 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131924 AN: 152138 Hom.: 57746 Cov.: 34

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.867 AC: 131988 AN: 152256 Hom.: 57761 Cov.: 34 AF XY: 0.871 AC XY: 64887 AN XY: 74468

African (AFR) AF: 0.731 AC: 30329 AN: 41506

American (AMR) AF: 0.919 AC: 14063 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3197 AN: 3472

East Asian (EAS) AF: 0.909 AC: 4709 AN: 5182

South Asian (SAS) AF: 0.876 AC: 4233 AN: 4830

European-Finnish (FIN) AF: 0.950 AC: 10091 AN: 10620

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62470 AN: 68022

Other (OTH) AF: 0.875 AC: 1851 AN: 2116

Alfa AF: 0.900 Hom.: 166211

Bravo AF: 0.860

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs7849014; hg19: chr9-139457506;