5-111091939-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507269.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253613	ENST00000507269.3	TSL:5	n.46+131C>T		intron	N/A
	ENSG00000253613	ENST00000741219.1		n.136+131C>T		intron	N/A
	ENSG00000253613	ENST00000741220.1		n.136+131C>T		intron	N/A

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

African (AFR) AF: 0.00195 AC: 13 AN: 6676

American (AMR) AF: 0.00704 AC: 59 AN: 8386

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 68 AN: 6178

East Asian (EAS) AF: 0.0000774 AC: 1 AN: 12926

South Asian (SAS) AF: 0.00242 AC: 61 AN: 25238

European-Finnish (FIN) AF: 0.0163 AC: 122 AN: 7500

Middle Eastern (MID) AF: 0.00866 AC: 7 AN: 808

European-Non Finnish (NFE) AF: 0.0107 AC: 1214 AN: 113988

Other (OTH) AF: 0.0116 AC: 129 AN: 11084

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

African (AFR) AF: 0.00231 AC: 96 AN: 41560

American (AMR) AF: 0.00981 AC: 150 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4822

European-Finnish (FIN) AF: 0.0236 AC: 251 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 797 AN: 68024

Other (OTH) AF: 0.00757 AC: 16 AN: 2114

Alfa AF: 0.00995 Hom.: 1

Bravo AF: 0.00840

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		0.046
PromoterAI		0.017	Neutral
Mutation Taster		=298/2	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs144605000; hg19: chr5-110427637;