2-21063185-T-C

Variant names:

• chr2-21063185-T-C
• rs515135
• ENST00000821616.1:n.240-13404A>G

Variant summary

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

The ENST00000821616.1(ENSG00000287956):​n.240-13404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,080 control chromosomes in the GnomAD database, including 42,268 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 0.73 (42268 hom., cov: 32)
• Consequence: ENSG00000287956 ENST00000821616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 153 publications found

Genes affected

ENSG00000287956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821616.1. 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
	ENSG00000287956	ENST00000821616.1		n.240-13404A>G		intron	N/A
	ENSG00000287956	ENST00000821617.1		n.262-5074A>G		intron	N/A
	ENSG00000287956	ENST00000821618.1		n.524+4174A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111442 AN: 151962 Hom.: 42257 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.733 AC: 111492 AN: 152080 Hom.: 42268 Cov.: 32 AF XY: 0.738 AC XY: 54864 AN XY: 74354

African (AFR) AF: 0.523 AC: 21679 AN: 41456

American (AMR) AF: 0.791 AC: 12091 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4664 AN: 5152

South Asian (SAS) AF: 0.860 AC: 4148 AN: 4826

European-Finnish (FIN) AF: 0.810 AC: 8568 AN: 10574

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55383 AN: 67996

Other (OTH) AF: 0.736 AC: 1554 AN: 2112

Alfa AF: 0.792 Hom.: 166826

Bravo AF: 0.719

Asia WGS AF: 0.872 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.27
PhyloP100		-0.39

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: rs515135;

hg19: chr2-21286057;