2-220365201-A-G

Position:

• chr2-220365201-A-G

Variant summary

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

The ENST00000432993.1(ENSG00000239498):​n.427+42980A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,910 control chromosomes in the GnomAD database, including 25,043 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 0.57 (25043 hom., cov: 32)
• Consequence: ENSG00000239498 ENST00000432993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

ENSG00000239498 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373893	XR_001739889.2	n.394+42980A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000239498	ENST00000432993.1	n.427+42980A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86057 AN: 151792 Hom.: 24994 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.567 AC: 86168 AN: 151910 Hom.: 25043 Cov.: 32 AF XY: 0.579 AC XY: 42965 AN XY: 74254

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.567

Alfa AF: 0.563 Hom.: 49816

Bravo AF: 0.551

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454535; hg19: chr2-221229922;