3-3314490-A-G

Variant names:

• chr3-3314490-A-G
• rs9874556
• ENST00000420000.6:n.537+22810T>C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.537+22810T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,924 control chromosomes in the GnomAD database, including 23,590 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 0.55 (23590 hom., cov: 31)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.777
• Publications: 5 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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
ENSG00000223727	ENST00000420000.6	n.537+22810T>C		intron_variant	Intron 4 of 4	4
ENSG00000223727	ENST00000451031.5	n.339+22810T>C		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83166 AN: 151806 Hom.: 23575 Cov.: 31

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.548 AC: 83232 AN: 151924 Hom.: 23590 Cov.: 31 AF XY: 0.554 AC XY: 41093 AN XY: 74234

African (AFR) AF: 0.521 AC: 21600 AN: 41434

American (AMR) AF: 0.597 AC: 9101 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1809 AN: 3468

East Asian (EAS) AF: 0.959 AC: 4967 AN: 5180

South Asian (SAS) AF: 0.681 AC: 3271 AN: 4806

European-Finnish (FIN) AF: 0.500 AC: 5269 AN: 10538

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35574 AN: 67934

Other (OTH) AF: 0.548 AC: 1158 AN: 2112

Alfa AF: 0.537 Hom.: 43151

Bravo AF: 0.552

Asia WGS AF: 0.804 AC: 2794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.52
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs9874556; hg19: chr3-3356174;