chr2-21286220-T-C

Variant names:

• chr2-21286220-T-C
• rs59014890
• ENST00000435237.1:n.120+64926T>C

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​n.120+64926T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,064 control chromosomes in the GnomAD database, including 5,940 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 0.27 (5940 hom., cov: 31)
• Consequence: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 4 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435237.1. 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
	ENSG00000231204	ENST00000435237.1	TSL:3	n.120+64926T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41195 AN: 151946 Hom.: 5927 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.271 AC: 41242 AN: 152064 Hom.: 5940 Cov.: 31 AF XY: 0.273 AC XY: 20288 AN XY: 74340

African (AFR) AF: 0.213 AC: 8811 AN: 41462

American (AMR) AF: 0.213 AC: 3248 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3466

East Asian (EAS) AF: 0.170 AC: 879 AN: 5166

South Asian (SAS) AF: 0.287 AC: 1380 AN: 4814

European-Finnish (FIN) AF: 0.353 AC: 3738 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21593 AN: 67974

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.285 Hom.: 795

Bravo AF: 0.254

Asia WGS AF: 0.222 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.080
DANN	Benign	0.42
PhyloP100		-2.7

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: rs59014890;

hg19: chr2-21509092;