rs3820706

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

Genes affected

ENSG00000225214 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420365.1. 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
	ENSG00000225214	ENST00000420365.1	TSL:3	n.120+2450T>C		intron	N/A
	ENSG00000299271	ENST00000762105.1		n.166-1010T>C		intron	N/A

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

African (AFR) AF: 0.224 AC: 9300 AN: 41476

American (AMR) AF: 0.100 AC: 1530 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3466

East Asian (EAS) AF: 0.566 AC: 2911 AN: 5144

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10578

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7045 AN: 68010

Other (OTH) AF: 0.149 AC: 314 AN: 2114

Alfa AF: 0.125 Hom.: 7383

Bravo AF: 0.160

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.50
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs3820706; hg19: chr2-152957411;