rs725472

Variant names:

• chr4-33892375-A-T
• rs725472
• ENST00000505326.6:n.298+3302A>T

Variant summary

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

The ENST00000506650.2(ENSG00000250723):​n.261+3302A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,138 control chromosomes in the GnomAD database, including 16,685 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 0.37 (16685 hom., cov: 32)
• Consequence: ENSG00000250723 ENST00000506650.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826

Genes affected

ENSG00000250723 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374392	XR_925180.3	n.315+130A>T		intron_variant	Intron 2 of 3
LOC105374392	XR_925181.3	n.353+130A>T		intron_variant	Intron 3 of 4
LOC105374392	XR_925182.3	n.208+324A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250723	ENST00000505326.6	n.298+3302A>T		intron_variant	Intron 2 of 2	4
ENSG00000250723	ENST00000506650.2	n.261+3302A>T		intron_variant	Intron 2 of 3	3
ENSG00000250954	ENST00000512581.5	n.164+55034T>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55457 AN: 152020 Hom.: 16630 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.365 AC: 55564 AN: 152138 Hom.: 16685 Cov.: 32 AF XY: 0.364 AC XY: 27066 AN XY: 74392

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.317

Alfa AF: 0.272 Hom.: 1235

Bravo AF: 0.391

Asia WGS AF: 0.377 AC: 1311 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725472; hg19: chr4-33893997;