rs904476

chr3-3341337-G-Achr3-3341337-G-Cchr3-3341337-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):n.374-3874C>T variant causes a intron, non coding transcript 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: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420000.6	n.374-3874C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.176-3874C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.233-3874C>T		intron_variant, non_coding_transcript_variant		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;