2-67637543-C-T

Variant names:

• chr2-67637543-C-T
• rs4141819
• ENST00000419809.1:n.126+46409G>A

Variant summary

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

The ENST00000419809.1(ENSG00000235495):​n.126+46409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,016 control chromosomes in the GnomAD database, including 39,294 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 0.72 (39294 hom., cov: 32)
• Consequence: ENSG00000235495 ENST00000419809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 27 publications found

Genes affected

ENSG00000235495 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374786	XR_001739524.2	n.65+13423G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235495	ENST00000419809.1	n.126+46409G>A		intron_variant	Intron 1 of 1	3
ENSG00000235495	ENST00000833509.1	n.82+13423G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108886 AN: 151898 Hom.: 39258 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.717 AC: 108983 AN: 152016 Hom.: 39294 Cov.: 32 AF XY: 0.720 AC XY: 53528 AN XY: 74308

African (AFR) AF: 0.711 AC: 29481 AN: 41460

American (AMR) AF: 0.777 AC: 11860 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2398 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4571 AN: 5156

South Asian (SAS) AF: 0.800 AC: 3858 AN: 4820

European-Finnish (FIN) AF: 0.688 AC: 7289 AN: 10592

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47256 AN: 67944

Other (OTH) AF: 0.703 AC: 1481 AN: 2106

Alfa AF: 0.702 Hom.: 119864

Bravo AF: 0.723

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs4141819; hg19: chr2-67864675;