rs353087

Variant names:

• chr3-15149080-T-C
• rs353087
• ENST00000723495.1:n.413-1312T>C

Variant summary

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

The ENST00000723495.1(ENSG00000294422):​n.413-1312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,038 control chromosomes in the GnomAD database, including 23,534 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 0.54 (23534 hom., cov: 32)
• Consequence: ENSG00000294422 ENST00000723495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 3 publications found

Genes affected

ENSG00000294422 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 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
ENSG00000294422	ENST00000723495.1	n.413-1312T>C		intron_variant	Intron 2 of 3
ENSG00000294422	ENST00000723496.1	n.459-1312T>C		intron_variant	Intron 3 of 4
ENSG00000294422	ENST00000723497.1	n.351-1312T>C		intron_variant	Intron 2 of 2
ENSG00000290932	ENST00000723644.1	n.260+2753A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81845 AN: 151920 Hom.: 23482 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.539 AC: 81962 AN: 152038 Hom.: 23534 Cov.: 32 AF XY: 0.544 AC XY: 40410 AN XY: 74298

African (AFR) AF: 0.751 AC: 31143 AN: 41484

American (AMR) AF: 0.523 AC: 7985 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1553 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3203 AN: 5174

South Asian (SAS) AF: 0.586 AC: 2819 AN: 4808

European-Finnish (FIN) AF: 0.486 AC: 5130 AN: 10550

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28449 AN: 67964

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.441 Hom.: 8752

Bravo AF: 0.549

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs353087; hg19: chr3-15190587;