rs9992275

Variant names:

• chr4-22130408-G-C
• rs9992275
• ENST00000510705.3:n.859+28778G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-22130408-G-C
• chr4-22130408-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510705.3(ENSG00000250039):​n.859+28778G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,990 control chromosomes in the GnomAD database, including 7,069 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 0.30 (7069 hom., cov: 32)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 1 publications found

Genes affected

ENSG00000250039 (HGNC:58742):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 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
ENSG00000250039	ENST00000510705.3	n.859+28778G>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45599 AN: 151872 Hom.: 7061 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.300 AC: 45647 AN: 151990 Hom.: 7069 Cov.: 32 AF XY: 0.303 AC XY: 22508 AN XY: 74274

African (AFR) AF: 0.305 AC: 12633 AN: 41474

American (AMR) AF: 0.320 AC: 4885 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3464

East Asian (EAS) AF: 0.262 AC: 1348 AN: 5136

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4808

European-Finnish (FIN) AF: 0.301 AC: 3177 AN: 10568

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19715 AN: 67964

Other (OTH) AF: 0.309 AC: 652 AN: 2112

Alfa AF: 0.181 Hom.: 360

Bravo AF: 0.297

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.59
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs9992275; hg19: chr4-22132031;