rs1458152

Positions:

• chr4-162775233-C-T

Variant summary

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

The ENST00000661387.1(ENSG00000248431):​n.165+33454C>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 0.957 in 152,156 control chromosomes in the GnomAD database, including 69,774 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 0.96 (69774 hom., cov: 32)
• Consequence: ENST00000661387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
	ENST00000661387.1	n.165+33454C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145541 AN: 152038 Hom.: 69740 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.957 AC: 145629 AN: 152156 Hom.: 69774 Cov.: 32 AF XY: 0.959 AC XY: 71345 AN XY: 74404

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.998

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.965

Alfa AF: 0.965 Hom.: 8808

Bravo AF: 0.956

Asia WGS AF: 0.964 AC: 3349 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458152; hg19: chr4-163696385;