rs2323306

Variant names:

• chr4-22076930-C-A
• rs2323306
• ENST00000510705.3:n.722+17570C>A

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.722+17570C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0831 in 152,218 control chromosomes in the GnomAD database, including 1,048 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 0.083 (1048 hom., cov: 32)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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.722+17570C>A		intron_variant	Intron 2 of 3	5
ENSG00000250039	ENST00000665391.1	n.492+17570C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0831 AC: 12635 AN: 152100 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0831 AC: 12653 AN: 152218 Hom.: 1048 Cov.: 32 AF XY: 0.0812 AC XY: 6041 AN XY: 74424

African (AFR) AF: 0.207 AC: 8573 AN: 41504

American (AMR) AF: 0.0479 AC: 733 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3472

East Asian (EAS) AF: 0.0539 AC: 279 AN: 5176

South Asian (SAS) AF: 0.122 AC: 586 AN: 4822

European-Finnish (FIN) AF: 0.0106 AC: 112 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2089 AN: 68024

Other (OTH) AF: 0.0677 AC: 143 AN: 2112

Alfa AF: 0.0436 Hom.: 380

Bravo AF: 0.0903

Asia WGS AF: 0.0770 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.70
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2323306; hg19: chr4-22078553;