9-104943907-C-T

Variant names:

• chr9-104943907-C-T
• rs2487030

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 0.173 in 152,012 control chromosomes in the GnomAD database, including 2,819 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 0.17 (2819 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.173 AC: 26311 AN: 151894 Hom.: 2824 Cov.: 31

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.173 AC: 26308 AN: 152012 Hom.: 2819 Cov.: 31 AF XY: 0.178 AC XY: 13242 AN XY: 74270

African (AFR) AF: 0.0502 AC: 2083 AN: 41486

American (AMR) AF: 0.173 AC: 2636 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1669 AN: 5148

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4810

European-Finnish (FIN) AF: 0.272 AC: 2868 AN: 10546

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14094 AN: 67984

Other (OTH) AF: 0.175 AC: 370 AN: 2114

Alfa AF: 0.193 Hom.: 5246

Bravo AF: 0.162

Asia WGS AF: 0.289 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.52
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2487030; hg19: chr9-107706188;