5-111080892-T-C

Variant names:

• chr5-111080892-T-C
• rs12110124
• ENST00000507269.3:n.213-3416A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507269.3(ENSG00000253613):​n.213-3416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,906 control chromosomes in the GnomAD database, including 9,762 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 0.35 (9762 hom., cov: 32)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 8 publications found

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 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
ENSG00000253613	ENST00000507269.3	n.213-3416A>G		intron_variant	Intron 2 of 3	5
ENSG00000253613	ENST00000741219.1	n.137-3847A>G		intron_variant	Intron 1 of 2
ENSG00000253613	ENST00000741220.1	n.137-4508A>G		intron_variant	Intron 1 of 1
ENSG00000253613	ENST00000741221.1	n.100-3847A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53396 AN: 151788 Hom.: 9744 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.360

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.352 AC: 53448 AN: 151906 Hom.: 9762 Cov.: 32 AF XY: 0.356 AC XY: 26459 AN XY: 74272

African (AFR) AF: 0.432 AC: 17905 AN: 41444

American (AMR) AF: 0.370 AC: 5656 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1407 AN: 5176

South Asian (SAS) AF: 0.393 AC: 1888 AN: 4808

European-Finnish (FIN) AF: 0.395 AC: 4168 AN: 10548

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20052 AN: 67868

Other (OTH) AF: 0.356 AC: 752 AN: 2112

Alfa AF: 0.225 Hom.: 629

Bravo AF: 0.354

Asia WGS AF: 0.330 AC: 1151 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.81
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs12110124; hg19: chr5-110416590;