rs4555772

Variant names:

• chr5-75006833-A-G
• rs4555772
• ENST00000509755.1:n.180T>C

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: ENSG00000249157 ENST00000509755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

Genes affected

ENSG00000249157 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249157	ENST00000509755.1	n.180T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000249856	ENST00000505200.1	n.212+10596T>C		intron_variant	Intron 2 of 4	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;