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. Variant got -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

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.374-3874C>T		intron_variant	Intron 3 of 4	4
ENSG00000223727	ENST00000451031.5	n.176-3874C>T		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.233-3874C>T		intron_variant	Intron 2 of 3	2

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

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.738

Alfa AF: 0.718 Hom.: 6262

Bravo AF: 0.704

Asia WGS AF: 0.781 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904476; hg19: chr3-3383021;