ENST00000717100.1:n.773-1575A>T

Variant names:

• chr2-29956980-T-A
• rs11688196
• ENST00000717100.1:n.773-1575A>T

Variant summary

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

The ENST00000717100.1(ENSG00000233862):​n.773-1575A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,972 control chromosomes in the GnomAD database, including 26,283 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 0.58 (26283 hom., cov: 31)
• Consequence: ENSG00000233862 ENST00000717100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 4 publications found

Genes affected

ENSG00000233862 (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 (NFE) allele frequency at 95% confidence interval = 0.628 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
ENSG00000233862	ENST00000717100.1	n.773-1575A>T		intron_variant	Intron 4 of 5
ENSG00000233862	ENST00000717101.1	n.444-1575A>T		intron_variant	Intron 4 of 4
ENSG00000233862	ENST00000769926.1	n.394-30621A>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88546 AN: 151852 Hom.: 26263 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.583 AC: 88603 AN: 151972 Hom.: 26283 Cov.: 31 AF XY: 0.580 AC XY: 43054 AN XY: 74260

African (AFR) AF: 0.548 AC: 22690 AN: 41440

American (AMR) AF: 0.556 AC: 8496 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1969 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2092 AN: 5174

South Asian (SAS) AF: 0.382 AC: 1838 AN: 4810

European-Finnish (FIN) AF: 0.628 AC: 6623 AN: 10542

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42979 AN: 67946

Other (OTH) AF: 0.582 AC: 1226 AN: 2106

Alfa AF: 0.612 Hom.: 3600

Bravo AF: 0.575

Asia WGS AF: 0.371 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.42
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs11688196; hg19: chr2-30179846;