ENST00000642129.1:n.*95+45392G>T

Variant names:

• chr1-56437871-C-A
• rs10789021
• ENST00000642129.1:n.*95+45392G>T

Variant summary

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

The ENST00000642129.1(ENSG00000284686):​n.*95+45392G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,060 control chromosomes in the GnomAD database, including 9,260 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 0.35 (9260 hom., cov: 32)
• Consequence: ENSG00000284686 ENST00000642129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284686	ENST00000642129.1		n.*95+45392G>T		intron	N/A	ENSP00000492927.1	A0A286YES4
	ENSG00000260971	ENST00000641035.1		n.555+39262G>T		intron	N/A
	ENSG00000284686	ENST00000641109.1		n.*321+41015G>T		intron	N/A	ENSP00000493138.1	A0A286YEZ7

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52690 AN: 151942 Hom.: 9261 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.347 AC: 52715 AN: 152060 Hom.: 9260 Cov.: 32 AF XY: 0.354 AC XY: 26298 AN XY: 74330

African (AFR) AF: 0.309 AC: 12796 AN: 41472

American (AMR) AF: 0.356 AC: 5448 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3466

East Asian (EAS) AF: 0.437 AC: 2261 AN: 5172

South Asian (SAS) AF: 0.452 AC: 2178 AN: 4814

European-Finnish (FIN) AF: 0.437 AC: 4620 AN: 10572

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23055 AN: 67962

Other (OTH) AF: 0.333 AC: 701 AN: 2106

Alfa AF: 0.333 Hom.: 18492

Bravo AF: 0.339

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10789021; hg19: chr1-56903543;