9-104948281-C-T

Variant names:

• chr9-104948281-C-T
• rs2472459

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 0.253 in 152,064 control chromosomes in the GnomAD database, including 5,084 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 0.25 (5084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 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: 0.253 AC: 38372 AN: 151946 Hom.: 5082 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.253 AC: 38407 AN: 152064 Hom.: 5084 Cov.: 32 AF XY: 0.256 AC XY: 18998 AN XY: 74330

African (AFR) AF: 0.325 AC: 13496 AN: 41474

American (AMR) AF: 0.202 AC: 3093 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1666 AN: 5170

South Asian (SAS) AF: 0.289 AC: 1396 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2858 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14189 AN: 67964

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.228 Hom.: 11427

Bravo AF: 0.252

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs2472459; hg19: chr9-107710562;