rs2362626

Variant names:

• chr3-190804092-G-C
• rs2362626
• ENST00000787366.1:n.219+3308C>G

Variant summary

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

The ENST00000787366.1(ENSG00000302498):​n.219+3308C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,156 control chromosomes in the GnomAD database, including 2,861 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 0.19 (2861 hom., cov: 32)
• Consequence: ENSG00000302498 ENST00000787366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

Genes affected

ENSG00000302498 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787366.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302498	ENST00000787366.1		n.219+3308C>G		intron	N/A
	ENSG00000302498	ENST00000787367.1		n.73+3694C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28212 AN: 152036 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.186 AC: 28249 AN: 152156 Hom.: 2861 Cov.: 32 AF XY: 0.192 AC XY: 14311 AN XY: 74360

African (AFR) AF: 0.169 AC: 7032 AN: 41530

American (AMR) AF: 0.204 AC: 3109 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1948 AN: 5168

South Asian (SAS) AF: 0.293 AC: 1415 AN: 4822

European-Finnish (FIN) AF: 0.272 AC: 2873 AN: 10580

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10850 AN: 67998

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.172 Hom.: 311

Bravo AF: 0.178

Asia WGS AF: 0.353 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2362626; hg19: chr3-190521881;