rs3813226

Variant names:

• chr2-73289653-G-A
• rs3813226
• ENST00000846694.1:n.174-8913G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-73289653-G-A
• chr2-73289653-G-C

Variant summary

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

The ENST00000846694.1(ENSG00000310032):​n.174-8913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,182 control chromosomes in the GnomAD database, including 3,909 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 0.18 (3909 hom., cov: 33)
• Consequence: ENSG00000310032 ENST00000846694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 2 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846694.1. 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
	ENSG00000310032	ENST00000846694.1		n.174-8913G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26834 AN: 152064 Hom.: 3895 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.177 AC: 26887 AN: 152182 Hom.: 3909 Cov.: 33 AF XY: 0.179 AC XY: 13307 AN XY: 74418

African (AFR) AF: 0.367 AC: 15202 AN: 41454

American (AMR) AF: 0.185 AC: 2831 AN: 15300

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

East Asian (EAS) AF: 0.425 AC: 2203 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1078 AN: 4824

European-Finnish (FIN) AF: 0.0556 AC: 590 AN: 10604

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

European-Non Finnish (NFE) AF: 0.0602 AC: 4097 AN: 68030

Other (OTH) AF: 0.165 AC: 348 AN: 2108

Alfa AF: 0.111 Hom.: 2670

Bravo AF: 0.198

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.49
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs3813226; hg19: chr2-73516781;