chr2-164893880-C-T

Variant names:

• chr2-164893880-C-T
• rs13424957
• ENST00000414885.2:n.639-18434C>T

Variant summary

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

The ENST00000414885.2(ENSG00000236283):​n.639-18434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,134 control chromosomes in the GnomAD database, including 883 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 0.060 (883 hom., cov: 32)
• Consequence: ENSG00000236283 ENST00000414885.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 12 publications found

Genes affected

ENSG00000236283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414885.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236283	ENST00000414885.2	TSL:5	n.639-18434C>T		intron	N/A
	ENSG00000236283	ENST00000638199.1	TSL:5	n.712+44478C>T		intron	N/A
	ENSG00000236283	ENST00000662281.1		n.561+44478C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0595 AC: 9052 AN: 152016 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00123

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0596 AC: 9071 AN: 152134 Hom.: 883 Cov.: 32 AF XY: 0.0577 AC XY: 4291 AN XY: 74368

African (AFR) AF: 0.202 AC: 8395 AN: 41488

American (AMR) AF: 0.0302 AC: 462 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10584

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00124 AC: 84 AN: 68008

Other (OTH) AF: 0.0493 AC: 104 AN: 2110

Alfa AF: 0.0273 Hom.: 829

Bravo AF: 0.0682

Asia WGS AF: 0.0130 AC: 48 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.076
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs13424957; hg19: chr2-165750390;