rs2181829

Variant names:

• chr9-2245401-G-A
• rs2181829
• ENST00000816240.1:n.219+1315G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-2245401-G-A
• chr9-2245401-G-C
• chr9-2245401-G-T

Variant summary

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

The ENST00000816240.1(ENSG00000306202):​n.219+1315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,184 control chromosomes in the GnomAD database, including 58,485 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 0.88 (58485 hom., cov: 31)
• Consequence: ENSG00000306202 ENST00000816240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 4 publications found

Genes affected

ENSG00000306202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816240.1. 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
	ENSG00000306202	ENST00000816240.1		n.219+1315G>A		intron	N/A
	ENSG00000306202	ENST00000816241.1		n.315+1315G>A		intron	N/A
	ENSG00000306202	ENST00000816242.1		n.246+1315G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133037 AN: 152066 Hom.: 58421 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.875 AC: 133161 AN: 152184 Hom.: 58485 Cov.: 31 AF XY: 0.876 AC XY: 65168 AN XY: 74382

African (AFR) AF: 0.953 AC: 39586 AN: 41542

American (AMR) AF: 0.879 AC: 13448 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2680 AN: 3468

East Asian (EAS) AF: 0.954 AC: 4934 AN: 5174

South Asian (SAS) AF: 0.903 AC: 4360 AN: 4826

European-Finnish (FIN) AF: 0.823 AC: 8695 AN: 10562

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56636 AN: 68006

Other (OTH) AF: 0.851 AC: 1795 AN: 2110

Alfa AF: 0.844 Hom.: 231312

Bravo AF: 0.884

Asia WGS AF: 0.902 AC: 3132 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs2181829; hg19: chr9-2245401;