9-96164845-C-T

Variant names:

• chr9-96164845-C-T
• rs2147256

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 0.351 in 151,946 control chromosomes in the GnomAD database, including 9,916 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 0.35 (9916 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• 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 (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.352 AC: 53381 AN: 151828 Hom.: 9916 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.351 AC: 53387 AN: 151946 Hom.: 9916 Cov.: 31 AF XY: 0.352 AC XY: 26149 AN XY: 74270

African (AFR) AF: 0.248 AC: 10286 AN: 41454

American (AMR) AF: 0.380 AC: 5800 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5162

South Asian (SAS) AF: 0.343 AC: 1649 AN: 4814

European-Finnish (FIN) AF: 0.441 AC: 4648 AN: 10548

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27209 AN: 67920

Other (OTH) AF: 0.354 AC: 747 AN: 2112

Alfa AF: 0.377 Hom.: 1496

Bravo AF: 0.339

Asia WGS AF: 0.280 AC: 973 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	0.40
DANN	Benign	0.53
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2147256; hg19: chr9-98927127;