2-226181626-T-C

Variant names:

• chr2-226181626-T-C
• rs2943644
• ENST00000423838.1:n.53-501A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423838.1(ENSG00000235070):​n.53-501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,968 control chromosomes in the GnomAD database, including 16,445 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 0.46 (16445 hom., cov: 32)
• Consequence: ENSG00000235070 ENST00000423838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

Genes affected

ENSG00000235070 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 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
ENSG00000235070	ENST00000423838.1	n.53-501A>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69293 AN: 151850 Hom.: 16427 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.456 AC: 69326 AN: 151968 Hom.: 16445 Cov.: 32 AF XY: 0.451 AC XY: 33526 AN XY: 74268

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.494

Alfa AF: 0.490 Hom.: 2798

Bravo AF: 0.451

Asia WGS AF: 0.576 AC: 2005 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2943644; hg19: chr2-227046342;