chr9-96164845-C-T

Variant names:

• chr9-96164845-C-T
• rs2147256

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.352 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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.354

Alfa AF: 0.382 Hom.: 1471

Bravo AF: 0.339

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2147256; hg19: chr9-98927127;