2-220366311-A-G

Variant names:

• chr2-220366311-A-G
• rs1378011
• ENST00000432993.1:n.427+44090A>G

Variant summary

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

The ENST00000432993.1(ENSG00000288902):​n.427+44090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,970 control chromosomes in the GnomAD database, including 25,239 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 (25239 hom., cov: 32)
• Consequence: ENSG00000288902 ENST00000432993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 2 publications found

Genes affected

ENSG00000288902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373893	XR_001739889.2	n.394+44090A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288902	ENST00000432993.1	n.427+44090A>G		intron_variant	Intron 2 of 3	3
ENSG00000288902	ENST00000830324.1	n.768+44136A>G		intron_variant	Intron 5 of 5
ENSG00000288902	ENST00000830325.1	n.442+41077A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86474 AN: 151850 Hom.: 25187 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.570 AC: 86591 AN: 151970 Hom.: 25239 Cov.: 32 AF XY: 0.581 AC XY: 43160 AN XY: 74268

African (AFR) AF: 0.509 AC: 21096 AN: 41480

American (AMR) AF: 0.550 AC: 8385 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2000 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4452 AN: 5124

South Asian (SAS) AF: 0.759 AC: 3658 AN: 4822

European-Finnish (FIN) AF: 0.673 AC: 7135 AN: 10596

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37875 AN: 67928

Other (OTH) AF: 0.567 AC: 1195 AN: 2108

Alfa AF: 0.560 Hom.: 2981

Bravo AF: 0.555

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.47
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1378011; hg19: chr2-221231032;