9-102972913-C-T

Variant names:

• chr9-102972913-C-T
• rs1342899

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 0.215 in 152,092 control chromosomes in the GnomAD database, including 4,470 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 0.21 (4470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 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: 0.215 AC: 32683 AN: 151974 Hom.: 4468 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.215 AC: 32697 AN: 152092 Hom.: 4470 Cov.: 32 AF XY: 0.219 AC XY: 16268 AN XY: 74348

African (AFR) AF: 0.0671 AC: 2789 AN: 41534

American (AMR) AF: 0.345 AC: 5261 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5170

South Asian (SAS) AF: 0.376 AC: 1814 AN: 4826

European-Finnish (FIN) AF: 0.217 AC: 2297 AN: 10572

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17623 AN: 67958

Other (OTH) AF: 0.256 AC: 541 AN: 2112

Alfa AF: 0.259 Hom.: 11000

Bravo AF: 0.218

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.67
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1342899; hg19: chr9-105735195;