2-221608107-C-T

Variant names:

• chr2-221608107-C-T
• rs925949
• ENST00000757163.1:n.152+26741C>T

Variant summary

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

The ENST00000757163.1(ENSG00000234446):​n.152+26741C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 147,014 control chromosomes in the GnomAD database, including 15,132 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 0.45 (15132 hom., cov: 23)
• Consequence: ENSG00000234446 ENST00000757163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 1 publications found

Genes affected

ENSG00000234446 (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 (SAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757163.1. 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
	ENSG00000234446	ENST00000757163.1		n.152+26741C>T		intron	N/A
	ENSG00000234446	ENST00000757166.1		n.152+26741C>T		intron	N/A
	ENSG00000234446	ENST00000757169.1		n.152+26741C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.447 AC: 65680 AN: 146914 Hom.: 15131 Cov.: 23

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.540

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.447 AC: 65689 AN: 147014 Hom.: 15132 Cov.: 23 AF XY: 0.453 AC XY: 32303 AN XY: 71244

African (AFR) AF: 0.329 AC: 13042 AN: 39582

American (AMR) AF: 0.461 AC: 6687 AN: 14500

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1551 AN: 3438

East Asian (EAS) AF: 0.506 AC: 2495 AN: 4930

South Asian (SAS) AF: 0.621 AC: 2885 AN: 4642

European-Finnish (FIN) AF: 0.555 AC: 5280 AN: 9506

Middle Eastern (MID) AF: 0.535 AC: 151 AN: 282

European-Non Finnish (NFE) AF: 0.479 AC: 32175 AN: 67204

Other (OTH) AF: 0.453 AC: 920 AN: 2032

Alfa AF: 0.442 Hom.: 1841

Bravo AF: 0.432

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.31
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs925949; hg19: chr2-222472827;