2-104542180-A-G

Variant names:

• chr2-104542180-A-G
• rs17624523
• ENST00000794889.1:n.230-370T>C

Variant summary

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

The ENST00000794889.1(ENSG00000303480):​n.230-370T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,090 control chromosomes in the GnomAD database, including 4,089 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 0.21 (4089 hom., cov: 32)
• Consequence: ENSG00000303480 ENST00000794889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781
• Publications: 7 publications found

Genes affected

ENSG00000303480 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 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
ENSG00000303480	ENST00000794889.1	n.230-370T>C		intron_variant	Intron 2 of 3
ENSG00000303480	ENST00000794890.1	n.230-370T>C		intron_variant	Intron 2 of 3
ENSG00000303480	ENST00000794894.1	n.662-370T>C		intron_variant	Intron 1 of 2
ENSG00000303480	ENST00000794895.1	n.290-370T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32005 AN: 151974 Hom.: 4091 Cov.: 32

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.210 AC: 32005 AN: 152090 Hom.: 4089 Cov.: 32 AF XY: 0.212 AC XY: 15773 AN XY: 74344

African (AFR) AF: 0.0718 AC: 2981 AN: 41510

American (AMR) AF: 0.224 AC: 3416 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1195 AN: 3466

East Asian (EAS) AF: 0.0681 AC: 352 AN: 5168

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4820

European-Finnish (FIN) AF: 0.266 AC: 2808 AN: 10566

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18746 AN: 67966

Other (OTH) AF: 0.229 AC: 484 AN: 2112

Alfa AF: 0.190 Hom.: 1467

Bravo AF: 0.198

Asia WGS AF: 0.179 AC: 620 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs17624523; hg19: chr2-105158638; COSMIC: COSV107165287;