chr5-111091939-G-A

Position:

• chr5-111091939-G-A

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, non coding transcript 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: ENST00000507269.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507269.3	n.46+131C>T		intron_variant, non_coding_transcript_variant		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;