3-3428776-C-T

Position:

• chr3-3428776-C-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-46126G>A 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 0.0399 in 152,172 control chromosomes in the GnomAD database, including 293 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 0.040 (293 hom., cov: 32)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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.201-46126G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.175+12132G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.60-46126G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6075 AN: 152054 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0399 AC: 6074 AN: 152172 Hom.: 293 Cov.: 32 AF XY: 0.0425 AC XY: 3158 AN XY: 74390

Gnomad4 AFR AF: 0.0252

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.0690

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0380 Hom.: 32

Bravo AF: 0.0437

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17031343; hg19: chr3-3470460;