rs4859315

chr4-33189747-T-C

Variant summary

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

The ENST00000653925.1(ENSG00000287968):n.38-12933T>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 0.0856 in 152,234 control chromosomes in the GnomAD database, including 741 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 0.086 (741 hom., cov: 33)
• Consequence: ENST00000653925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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
	ENST00000653925.1	n.38-12933T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13044 AN: 152114 Hom.: 744 Cov.: 33

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0856 AC: 13026 AN: 152234 Hom.: 741 Cov.: 33 AF XY: 0.0901 AC XY: 6703 AN XY: 74430

Gnomad4 AFR AF: 0.0238

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.0886

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0996 Hom.: 246

Bravo AF: 0.0751

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.0
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4859315; hg19: chr4-33191369;