2-88824725-T-C

Variant names:

• chr2-88824725-T-C
• rs1843217
• ENST00000434790.2:n.232+251A>G

Variant summary

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

The ENST00000434790.2(ENSG00000290802):​n.232+251A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,102 control chromosomes in the GnomAD database, including 888 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 0.10 (888 hom., cov: 32)
• Consequence: ENSG00000290802 ENST00000434790.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 6 publications found

Genes affected

ENSG00000290802 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434790.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290802	ENST00000434790.2	TSL:5	n.232+251A>G		intron	N/A
	ENSG00000240040	ENST00000624935.3	TSL:2	n.40-6296A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15757 AN: 151984 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.104 AC: 15775 AN: 152102 Hom.: 888 Cov.: 32 AF XY: 0.101 AC XY: 7534 AN XY: 74350

African (AFR) AF: 0.145 AC: 6031 AN: 41480

American (AMR) AF: 0.0933 AC: 1426 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3468

East Asian (EAS) AF: 0.0384 AC: 198 AN: 5158

South Asian (SAS) AF: 0.0722 AC: 347 AN: 4808

European-Finnish (FIN) AF: 0.0835 AC: 885 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0945 AC: 6424 AN: 67994

Other (OTH) AF: 0.0810 AC: 171 AN: 2112

Alfa AF: 0.0946 Hom.: 1375

Bravo AF: 0.107

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.71
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1843217; hg19: chr2-89124238;