rs4555772

chr5-75006833-A-G

Variant summary

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

The ENST00000509755.1(ENSG00000249157):n.180T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 394,594 control chromosomes in the GnomAD database, including 38,582 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 0.47 (18136 hom., cov: 31)
  • Exomes 𝑓: 0.41 (20446 hom.)
• Consequence: ENST00000509755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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
	ENST00000509755.1	n.180T>C		non_coding_transcript_exon_variant	1/1
	ENST00000505200.1	n.212+10596T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70970 AN: 151808 Hom.: 18103 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.451

GnomAD4 exome AF: 0.407 AC: 98690 AN: 242668 Hom.: 20446 Cov.: 0 AF XY: 0.411 AC XY: 52489 AN XY: 127762

Gnomad4 AFR exome AF: 0.680

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.384

Gnomad4 EAS exome AF: 0.393

Gnomad4 SAS exome AF: 0.560

Gnomad4 FIN exome AF: 0.391

Gnomad4 NFE exome AF: 0.376

Gnomad4 OTH exome AF: 0.409

GnomAD4 genome AF: 0.468 AC: 71070 AN: 151926 Hom.: 18136 Cov.: 31 AF XY: 0.467 AC XY: 34644 AN XY: 74246

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.449

Alfa AF: 0.389 Hom.: 21202

Bravo AF: 0.482

Asia WGS AF: 0.461 AC: 1603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.6
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4555772; hg19: chr5-74302658;