rs156501

chr4-154757193-C-T

Variant summary

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

The ENST00000515071.1(ENSG00000249041):n.417-2329G>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 0.249 in 152,096 control chromosomes in the GnomAD database, including 4,964 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 0.25 (4964 hom., cov: 32)
• Consequence: ENST00000515071.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 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
	ENST00000515071.1	n.417-2329G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37826 AN: 151978 Hom.: 4951 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.249 AC: 37871 AN: 152096 Hom.: 4964 Cov.: 32 AF XY: 0.257 AC XY: 19102 AN XY: 74322

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.235

Alfa AF: 0.217 Hom.: 7974

Bravo AF: 0.248

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.17
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs156501; hg19: chr4-155678345;