rs2323262

Variant names:

• chr4-22142813-G-A
• rs2323262
• ENST00000510705.3:n.859+41183G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510705.3(ENSG00000250039):​n.859+41183G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,042 control chromosomes in the GnomAD database, including 2,327 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 0.16 (2327 hom., cov: 32)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

ENSG00000250039 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 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+41183G>A		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24278 AN: 151924 Hom.: 2324 Cov.: 32

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.160 AC: 24288 AN: 152042 Hom.: 2327 Cov.: 32 AF XY: 0.164 AC XY: 12177 AN XY: 74326

Gnomad4 AFR AF: 0.0575

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.177

Alfa AF: 0.187 Hom.: 1405

Bravo AF: 0.152

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2323262; hg19: chr4-22144436;