ENST00000656081.1:n.2257-1058A>T

Variant names:

• chr5-1348683-A-T
• rs37011
• ENST00000656081.1:n.2257-1058A>T

Variant summary

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

The ENST00000656081.1(ENSG00000286388):​n.2257-1058A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,090 control chromosomes in the GnomAD database, including 13,988 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 (13988 hom., cov: 33)
• Consequence: ENSG00000286388 ENST00000656081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 11 publications found

Genes affected

ENSG00000286388 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656081.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286388	ENST00000656081.1		n.2257-1058A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64072 AN: 151972 Hom.: 13981 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.422 AC: 64117 AN: 152090 Hom.: 13988 Cov.: 33 AF XY: 0.414 AC XY: 30792 AN XY: 74338

African (AFR) AF: 0.486 AC: 20172 AN: 41476

American (AMR) AF: 0.329 AC: 5032 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3468

East Asian (EAS) AF: 0.182 AC: 945 AN: 5180

South Asian (SAS) AF: 0.203 AC: 977 AN: 4822

European-Finnish (FIN) AF: 0.447 AC: 4728 AN: 10576

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29367 AN: 67962

Other (OTH) AF: 0.413 AC: 873 AN: 2116

Alfa AF: 0.427 Hom.: 1725

Bravo AF: 0.419

Asia WGS AF: 0.222 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.82
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs37011; hg19: chr5-1348798;