5-75006833-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

ENSG00000249157 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.680 AC: 3831 AN: 5634

American (AMR) AF: 0.462 AC: 5753 AN: 12454

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 2597 AN: 6760

East Asian (EAS) AF: 0.393 AC: 5505 AN: 13990

South Asian (SAS) AF: 0.560 AC: 9729 AN: 17380

European-Finnish (FIN) AF: 0.391 AC: 12865 AN: 32890

Middle Eastern (MID) AF: 0.462 AC: 1204 AN: 2608

European-Non Finnish (NFE) AF: 0.376 AC: 51631 AN: 137332

Other (OTH) AF: 0.409 AC: 5575 AN: 13620

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

African (AFR) AF: 0.685 AC: 28378 AN: 41404

American (AMR) AF: 0.422 AC: 6435 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1288 AN: 3464

East Asian (EAS) AF: 0.385 AC: 1988 AN: 5158

South Asian (SAS) AF: 0.548 AC: 2637 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4074 AN: 10554

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24736 AN: 67962

Other (OTH) AF: 0.449 AC: 944 AN: 2102

Alfa AF: 0.401 Hom.: 44507

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
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4555772; hg19: chr5-74302658;