rs12053210

Variant names:

• chr2-239788590-A-T
• rs12053210
• ENST00000407524.1:n.195+8165A>T

Variant summary

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

The ENST00000407524.1(ENSG00000220256):​n.195+8165A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,272 control chromosomes in the GnomAD database, including 1,083 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 0.11 (1083 hom., cov: 33)
• Consequence: ENSG00000220256 ENST00000407524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 3 publications found

Genes affected

ENSG00000220256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407524.1. 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
	LOC150935	NR_037808.1		n.195+8165A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000220256	ENST00000407524.1	TSL:2	n.195+8165A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16944 AN: 152154 Hom.: 1085 Cov.: 33

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0916

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.111 AC: 16938 AN: 152272 Hom.: 1083 Cov.: 33 AF XY: 0.115 AC XY: 8530 AN XY: 74442

African (AFR) AF: 0.0521 AC: 2167 AN: 41562

American (AMR) AF: 0.0914 AC: 1399 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3470

East Asian (EAS) AF: 0.151 AC: 781 AN: 5176

South Asian (SAS) AF: 0.175 AC: 846 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1733 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9378 AN: 68020

Other (OTH) AF: 0.114 AC: 241 AN: 2112

Alfa AF: 0.115 Hom.: 148

Bravo AF: 0.102

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		-0.15

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: rs12053210;

hg19: chr2-240710284;