chr2-220977972-G-A

Variant names:

• chr2-220977972-G-A
• rs1369330
• ENST00000830589.1:n.196-40812C>T

Variant summary

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

The ENST00000830589.1(ENSG00000286272):​n.196-40812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,034 control chromosomes in the GnomAD database, including 13,101 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 0.39 (13101 hom., cov: 32)
• Consequence: ENSG00000286272 ENST00000830589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 1 publications found

Genes affected

ENSG00000286272 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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
ENSG00000286272	ENST00000830589.1	n.196-40812C>T		intron_variant	Intron 2 of 4
ENSG00000286272	ENST00000830590.1	n.199-40812C>T		intron_variant	Intron 2 of 3
ENSG00000286272	ENST00000830591.1	n.146-40812C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59785 AN: 151916 Hom.: 13102 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.393 AC: 59808 AN: 152034 Hom.: 13101 Cov.: 32 AF XY: 0.392 AC XY: 29148 AN XY: 74310

African (AFR) AF: 0.194 AC: 8059 AN: 41496

American (AMR) AF: 0.443 AC: 6760 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2022 AN: 5164

South Asian (SAS) AF: 0.352 AC: 1697 AN: 4820

European-Finnish (FIN) AF: 0.469 AC: 4948 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33144 AN: 67944

Other (OTH) AF: 0.417 AC: 881 AN: 2112

Alfa AF: 0.430 Hom.: 1830

Bravo AF: 0.386

Asia WGS AF: 0.423 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.20
DANN	Benign	0.62
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1369330; hg19: chr2-221842692;