2-203904331-A-G

Variant names:

• chr2-203904331-A-G
• rs3116504
• ENST00000810800.1:n.203+7326A>G

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.203+7326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 147,398 control chromosomes in the GnomAD database, including 10,954 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 0.38 (10954 hom., cov: 33)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 10 publications found

Genes affected

ENSG00000305408 (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 (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305408	ENST00000810800.1		n.203+7326A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 56311 AN: 147282 Hom.: 10943 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.382 AC: 56369 AN: 147398 Hom.: 10954 Cov.: 33 AF XY: 0.389 AC XY: 27975 AN XY: 71832

African (AFR) AF: 0.431 AC: 17225 AN: 39952

American (AMR) AF: 0.405 AC: 5906 AN: 14584

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 864 AN: 3394

East Asian (EAS) AF: 0.595 AC: 3041 AN: 5110

South Asian (SAS) AF: 0.251 AC: 1108 AN: 4412

European-Finnish (FIN) AF: 0.506 AC: 5163 AN: 10202

Middle Eastern (MID) AF: 0.210 AC: 61 AN: 290

European-Non Finnish (NFE) AF: 0.330 AC: 21982 AN: 66556

Other (OTH) AF: 0.337 AC: 675 AN: 2004

Alfa AF: 0.327 Hom.: 5318

Bravo AF: 0.369

Asia WGS AF: 0.374 AC: 1297 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	3.7
DANN	Benign	0.49
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs3116504; hg19: chr2-204769054;