ENST00000648979.2:n.116+44294C>T

Variant names:

• chr3-148547524-G-A
• rs2091023
• ENST00000648979.2:n.116+44294C>T

Variant summary

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

The ENST00000648979.2(ENSG00000285557):​n.116+44294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,812 control chromosomes in the GnomAD database, including 13,456 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 0.42 (13456 hom., cov: 31)
• Consequence: ENSG00000285557 ENST00000648979.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 3 publications found

Genes affected

ENSG00000285557 (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 (NFE) allele frequency at 95% confidence interval = 0.465 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
ENSG00000285557	ENST00000648979.2	n.116+44294C>T		intron_variant	Intron 1 of 5
ENSG00000285557	ENST00000752703.1	n.119-39144C>T		intron_variant	Intron 1 of 6
ENSG00000285557	ENST00000752704.1	n.116+44294C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62990 AN: 151692 Hom.: 13445 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.415 AC: 63031 AN: 151812 Hom.: 13456 Cov.: 31 AF XY: 0.411 AC XY: 30474 AN XY: 74156

African (AFR) AF: 0.347 AC: 14358 AN: 41396

American (AMR) AF: 0.404 AC: 6152 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1483 AN: 3466

East Asian (EAS) AF: 0.290 AC: 1492 AN: 5146

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4812

European-Finnish (FIN) AF: 0.433 AC: 4561 AN: 10528

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31907 AN: 67924

Other (OTH) AF: 0.426 AC: 897 AN: 2108

Alfa AF: 0.429 Hom.: 2792

Bravo AF: 0.410

Asia WGS AF: 0.332 AC: 1157 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	2.6
DANN	Benign	0.75
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs2091023; hg19: chr3-148265311;