rs2323262

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.94).
• 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

African (AFR) AF: 0.0575 AC: 2389 AN: 41514

American (AMR) AF: 0.213 AC: 3246 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1295 AN: 5144

South Asian (SAS) AF: 0.298 AC: 1439 AN: 4822

European-Finnish (FIN) AF: 0.227 AC: 2396 AN: 10576

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12394 AN: 67968

Other (OTH) AF: 0.177 AC: 372 AN: 2106

Alfa AF: 0.184 Hom.: 1502

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
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs2323262; hg19: chr4-22144436;