rs904476

Variant names:

• chr3-3341337-G-A
• rs904476
• ENST00000420000.6:n.374-3874C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-3341337-G-A
• chr3-3341337-G-C
• chr3-3341337-G-T

Variant summary

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

The ENST00000455703.1(ENSG00000223727):​n.233-3874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,086 control chromosomes in the GnomAD database, including 38,918 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 0.71 (38918 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455703.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.374-3874C>T		intron	N/A
	ENSG00000223727	ENST00000451031.5	TSL:3	n.176-3874C>T		intron	N/A
	ENSG00000223727	ENST00000455703.1	TSL:2	n.233-3874C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107944 AN: 151966 Hom.: 38900 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.710 AC: 108007 AN: 152086 Hom.: 38918 Cov.: 32 AF XY: 0.717 AC XY: 53298 AN XY: 74342

African (AFR) AF: 0.580 AC: 24049 AN: 41472

American (AMR) AF: 0.787 AC: 12015 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3472

East Asian (EAS) AF: 0.776 AC: 3999 AN: 5152

South Asian (SAS) AF: 0.874 AC: 4209 AN: 4814

European-Finnish (FIN) AF: 0.769 AC: 8147 AN: 10594

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50291 AN: 67994

Other (OTH) AF: 0.738 AC: 1558 AN: 2112

Alfa AF: 0.715 Hom.: 6417

Bravo AF: 0.704

Asia WGS AF: 0.781 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs904476; hg19: chr3-3383021;