ENST00000554318.2:n.324+27112G>A

Variant names:

• chr15-93620471-G-A
• rs4350528
• ENST00000554318.2:n.324+27112G>A

Variant summary

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

The ENST00000554318.2(ENSG00000257060):​n.324+27112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,970 control chromosomes in the GnomAD database, including 25,874 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 0.52 (25874 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000554318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 4 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983974	XR_001751681.2	n.1032+27738G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000554318.2	n.324+27112G>A		intron_variant	Intron 3 of 3	3
ENSG00000257060	ENST00000653322.2	n.964+27738G>A		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79480 AN: 151852 Hom.: 25868 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.523 AC: 79496 AN: 151970 Hom.: 25874 Cov.: 32 AF XY: 0.516 AC XY: 38350 AN XY: 74274

African (AFR) AF: 0.134 AC: 5551 AN: 41462

American (AMR) AF: 0.611 AC: 9322 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1731 AN: 5156

South Asian (SAS) AF: 0.577 AC: 2772 AN: 4802

European-Finnish (FIN) AF: 0.563 AC: 5941 AN: 10544

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49603 AN: 67954

Other (OTH) AF: 0.586 AC: 1239 AN: 2114

Alfa AF: 0.663 Hom.: 88829

Bravo AF: 0.509

Asia WGS AF: 0.456 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.60
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4350528; hg19: chr15-94163700;