rs2383700

Variant names:

• chr9-26581768-C-T
• rs2383700

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 0.0451 in 152,030 control chromosomes in the GnomAD database, including 279 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 0.045 (279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.102 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: 0.0450 AC: 6832 AN: 151912 Hom.: 277 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0258

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00964

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0427

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

GnomAD4 genome AF: 0.0451 AC: 6857 AN: 152030 Hom.: 279 Cov.: 32 AF XY: 0.0442 AC XY: 3287 AN XY: 74296

African (AFR) AF: 0.105 AC: 4343 AN: 41486

American (AMR) AF: 0.0257 AC: 392 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.00966 AC: 50 AN: 5174

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4826

European-Finnish (FIN) AF: 0.0160 AC: 170 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0207 AC: 1409 AN: 67932

Other (OTH) AF: 0.0423 AC: 89 AN: 2106

Alfa AF: 0.0283 Hom.: 45

Bravo AF: 0.0480

Asia WGS AF: 0.0210 AC: 73 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	0.79
DANN	Benign	0.46
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2383700; hg19: chr9-26581766;