3-6093149-T-C

Variant summary

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

The ENST00000425894.1(ENSG00000229642):n.323-30827T>C 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 0.836 in 152,150 control chromosomes in the GnomAD database, including 53,496 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 0.84 (53496 hom., cov: 31)
• Consequence: ENST00000425894.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

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 (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376942	XR_940578.3	n.582+19804T>C		intron_variant, non_coding_transcript_variant
LOC105376942	XR_940579.2	n.582+19804T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000425894.1	n.323-30827T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127142 AN: 152032 Hom.: 53434 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.836 AC: 127264 AN: 152150 Hom.: 53496 Cov.: 31 AF XY: 0.837 AC XY: 62271 AN XY: 74364

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.843

Alfa AF: 0.812 Hom.: 31544

Bravo AF: 0.836

Asia WGS AF: 0.823 AC: 2863 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	1.4
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504034; hg19: chr3-6134836;