chr2-207489233-T-G

Position:

• chr2-207489233-T-G

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+28387A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 138,458 control chromosomes in the GnomAD database, including 5,321 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 0.19 (5321 hom., cov: 27)
• Consequence: ENSG00000223725 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

ENSG00000223725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000223725	ENST00000412387.5	n.260+28387A>C		intron_variant		4
ENSG00000223725	ENST00000418850.1	n.256+28387A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.194 AC: 26903 AN: 138364 Hom.: 5324 Cov.: 27

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.194 AC: 26908 AN: 138458 Hom.: 5321 Cov.: 27 AF XY: 0.194 AC XY: 13035 AN XY: 67270

Gnomad4 AFR AF: 0.0613

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0948 Hom.: 295

Asia WGS AF: 0.164 AC: 571 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs80140096; hg19: chr2-208353957;