ENST00000810800.1:n.63+1225A>G

Variant names:

• chr2-203882044-A-G
• rs11571300
• ENST00000810800.1:n.63+1225A>G

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.63+1225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,132 control chromosomes in the GnomAD database, including 1,093 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 0.11 (1093 hom., cov: 32)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 9 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=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305408	ENST00000810800.1		n.63+1225A>G		intron	N/A
	ENSG00000305408	ENST00000810801.1		n.83+1225A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16185 AN: 152014 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.106 AC: 16189 AN: 152132 Hom.: 1093 Cov.: 32 AF XY: 0.106 AC XY: 7887 AN XY: 74352

African (AFR) AF: 0.0286 AC: 1187 AN: 41524

American (AMR) AF: 0.134 AC: 2049 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3470

East Asian (EAS) AF: 0.123 AC: 637 AN: 5174

South Asian (SAS) AF: 0.140 AC: 670 AN: 4792

European-Finnish (FIN) AF: 0.119 AC: 1256 AN: 10576

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9480 AN: 68000

Other (OTH) AF: 0.130 AC: 273 AN: 2108

Alfa AF: 0.130 Hom.: 1755

Bravo AF: 0.104

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs11571300; hg19: chr2-204746767;