rs3813224

Variant names:

• chr2-73289636-A-C
• rs3813224
• ENST00000846694.1:n.174-8930A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-73289636-A-C
• chr2-73289636-A-T

Variant summary

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

The ENST00000846694.1(ENSG00000310032):​n.174-8930A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,044 control chromosomes in the GnomAD database, including 4,479 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 (4479 hom., cov: 33)
• Consequence: ENSG00000310032 ENST00000846694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 1 publications found

Genes affected

ENSG00000310032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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
ENSG00000310032	ENST00000846694.1	n.174-8930A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28439 AN: 151926 Hom.: 4460 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.187 AC: 28505 AN: 152044 Hom.: 4479 Cov.: 33 AF XY: 0.189 AC XY: 14063 AN XY: 74338

African (AFR) AF: 0.405 AC: 16761 AN: 41360

American (AMR) AF: 0.189 AC: 2886 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2177 AN: 5152

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4826

European-Finnish (FIN) AF: 0.0555 AC: 589 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4106 AN: 68012

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.124 Hom.: 4285

Bravo AF: 0.211

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.79
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs3813224; hg19: chr2-73516764;