rs3820706

Variant names:

• chr2-152100897-T-C
• rs3820706
• ENST00000420365.1:n.120+2450T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420365.1(ENSG00000225214):​n.120+2450T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,100 control chromosomes in the GnomAD database, including 2,888 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 0.17 (2888 hom., cov: 32)
• Consequence: ENSG00000225214 ENST00000420365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

ENSG00000225214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 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
ENSG00000225214	ENST00000420365.1	n.120+2450T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25303 AN: 151982 Hom.: 2884 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.167 AC: 25336 AN: 152100 Hom.: 2888 Cov.: 32 AF XY: 0.173 AC XY: 12883 AN XY: 74352

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.149

Alfa AF: 0.118 Hom.: 2954

Bravo AF: 0.160

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3820706; hg19: chr2-152957411;