2-128332535-C-T

Variant names:

• chr2-128332535-C-T
• rs11890277
• ENST00000782091.1:n.64+14882C>T

Variant summary

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

The ENST00000782091.1(ENSG00000301826):​n.64+14882C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,110 control chromosomes in the GnomAD database, including 1,345 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 0.13 (1345 hom., cov: 33)
• Consequence: ENSG00000301826 ENST00000782091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 8 publications found

Genes affected

ENSG00000301826 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782091.1. 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
	ENSG00000301826	ENST00000782091.1		n.64+14882C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19350 AN: 151992 Hom.: 1341 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.127 AC: 19365 AN: 152110 Hom.: 1345 Cov.: 33 AF XY: 0.132 AC XY: 9808 AN XY: 74354

African (AFR) AF: 0.112 AC: 4639 AN: 41514

American (AMR) AF: 0.201 AC: 3069 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3472

East Asian (EAS) AF: 0.174 AC: 903 AN: 5180

South Asian (SAS) AF: 0.201 AC: 970 AN: 4820

European-Finnish (FIN) AF: 0.153 AC: 1615 AN: 10568

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7158 AN: 67968

Other (OTH) AF: 0.133 AC: 281 AN: 2112

Alfa AF: 0.111 Hom.: 4554

Bravo AF: 0.130

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.91
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11890277;

hg19: chr2-129090109;