4-19781529-C-T

Variant summary

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

The ENST00000511431.1(ENSG00000248515):n.289-74747C>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 0.13 in 152,122 control chromosomes in the GnomAD database, including 1,529 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 0.13 (1529 hom., cov: 32)
• Consequence: ENST00000511431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 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
	ENST00000511431.1	n.289-74747C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000655810.1	n.33-74747C>T		intron_variant, non_coding_transcript_variant
	ENST00000661892.1	n.227-52396C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19833 AN: 152004 Hom.: 1528 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0749

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.130 AC: 19824 AN: 152122 Hom.: 1529 Cov.: 32 AF XY: 0.128 AC XY: 9537 AN XY: 74358

Gnomad4 AFR AF: 0.0660

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0750

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.134

Alfa AF: 0.147 Hom.: 1007

Bravo AF: 0.124

Asia WGS AF: 0.0440 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.81
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11936151; hg19: chr4-19783152;