ENST00000642129.1:n.*96-33310T>A

Variant names:

• chr1-56282510-A-T
• rs1557061
• ENST00000642129.1:n.*96-33310T>A

Variant summary

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

The ENST00000642129.1(ENSG00000284686):​n.*96-33310T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,026 control chromosomes in the GnomAD database, including 10,533 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 0.36 (10533 hom., cov: 32)
• Consequence: ENSG00000284686 ENST00000642129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598
• Publications: 2 publications found

Genes affected

ENSG00000284686 (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 (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642129.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284686	ENST00000642129.1		n.*96-33310T>A		intron	N/A	ENSP00000492927.1
	ENSG00000260971	ENST00000641035.1		n.556-33310T>A		intron	N/A
	ENSG00000284686	ENST00000641109.1		n.*322-33310T>A		intron	N/A	ENSP00000493138.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54424 AN: 151908 Hom.: 10524 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.358 AC: 54443 AN: 152026 Hom.: 10533 Cov.: 32 AF XY: 0.361 AC XY: 26840 AN XY: 74282

African (AFR) AF: 0.219 AC: 9102 AN: 41478

American (AMR) AF: 0.406 AC: 6194 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2520 AN: 5160

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4812

European-Finnish (FIN) AF: 0.485 AC: 5120 AN: 10566

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27942 AN: 67960

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.247 Hom.: 637

Bravo AF: 0.350

Asia WGS AF: 0.335 AC: 1163 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	5.1
DANN	Benign	0.76
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs1557061; hg19: chr1-56748182;