rs4452212

Variant names:

• chr2-136258421-G-A
• rs4452212
• ENST00000837573.1:n.120+11896G>A

Variant summary

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

The ENST00000837573.1(ENSG00000308974):​n.120+11896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,132 control chromosomes in the GnomAD database, including 14,505 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 0.37 (14505 hom., cov: 32)
• Consequence: ENSG00000308974 ENST00000837573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 23 publications found

Genes affected

ENSG00000308974 (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 (NFE) allele frequency at 95% confidence interval = 0.563 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
ENSG00000308974	ENST00000837573.1	n.120+11896G>A		intron_variant	Intron 1 of 1
ENSG00000308974	ENST00000837574.1	n.284+4277G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56187 AN: 152014 Hom.: 14509 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.369 AC: 56174 AN: 152132 Hom.: 14505 Cov.: 32 AF XY: 0.362 AC XY: 26894 AN XY: 74372

African (AFR) AF: 0.111 AC: 4619 AN: 41520

American (AMR) AF: 0.222 AC: 3384 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3466

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5182

South Asian (SAS) AF: 0.238 AC: 1151 AN: 4830

European-Finnish (FIN) AF: 0.618 AC: 6536 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38618 AN: 67974

Other (OTH) AF: 0.271 AC: 572 AN: 2114

Alfa AF: 0.481 Hom.: 50264

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.74
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4452212; hg19: chr2-137015991;