chr2-155072930-G-A

Variant names:

• chr2-155072930-G-A
• rs1482308
• ENST00000766622.1:n.429-36916C>T

Variant summary

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

The ENST00000766622.1(ENSG00000230991):​n.429-36916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,856 control chromosomes in the GnomAD database, including 6,105 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 0.27 (6105 hom., cov: 31)
• Consequence: ENSG00000230991 ENST00000766622.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 4 publications found

Genes affected

ENSG00000230991 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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
ENSG00000230991	ENST00000766622.1	n.429-36916C>T		intron_variant	Intron 3 of 5
ENSG00000230991	ENST00000766623.1	n.420-36916C>T		intron_variant	Intron 3 of 4
ENSG00000299825	ENST00000766678.1	n.297-10157G>A		intron_variant	Intron 1 of 1
ENSG00000299825	ENST00000766679.1	n.270+6655G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41349 AN: 151738 Hom.: 6100 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.272 AC: 41370 AN: 151856 Hom.: 6105 Cov.: 31 AF XY: 0.272 AC XY: 20164 AN XY: 74200

African (AFR) AF: 0.175 AC: 7271 AN: 41440

American (AMR) AF: 0.266 AC: 4048 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2179 AN: 5126

South Asian (SAS) AF: 0.315 AC: 1513 AN: 4810

European-Finnish (FIN) AF: 0.294 AC: 3107 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21393 AN: 67908

Other (OTH) AF: 0.281 AC: 592 AN: 2110

Alfa AF: 0.302 Hom.: 3746

Bravo AF: 0.268

Asia WGS AF: 0.352 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1482308; hg19: chr2-155929442; COSMIC: COSV64715840;