rs144605000

Variant names:

• chr5-111091939-G-A
• rs144605000
• ENST00000507269.3:n.46+131C>T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000507269.3(ENSG00000253613):​n.46+131C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00899 in 345,078 control chromosomes in the GnomAD database, including 26 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 0.0094 (12 hom., cov: 33)
  • Exomes 𝑓: 0.0087 (14 hom.)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAd4 at 12 gene

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
ENSG00000253613	ENST00000507269.3	n.46+131C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.00939 AC: 1429 AN: 152176 Hom.: 12 Cov.: 33

Gnomad AFR AF: 0.00232

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.00982

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.00765

GnomAD4 exome AF: 0.00868 AC: 1674 AN: 192784 Hom.: 14 Cov.: 0 AF XY: 0.00837 AC XY: 838 AN XY: 100094

Gnomad4 AFR exome AF: 0.00195

Gnomad4 AMR exome AF: 0.00704

Gnomad4 ASJ exome AF: 0.0110

Gnomad4 EAS exome AF: 0.0000774

Gnomad4 SAS exome AF: 0.00242

Gnomad4 FIN exome AF: 0.0163

Gnomad4 NFE exome AF: 0.0107

Gnomad4 OTH exome AF: 0.0116

GnomAD4 genome AF: 0.00938 AC: 1429 AN: 152294 Hom.: 12 Cov.: 33 AF XY: 0.00943 AC XY: 702 AN XY: 74460

Gnomad4 AFR AF: 0.00231

Gnomad4 AMR AF: 0.00981

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.00757

Alfa AF: 0.00975 Hom.: 1

Bravo AF: 0.00840

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs144605000; hg19: chr5-110427637;