5-68733251-A-C

Variant names:

• chr5-68733251-A-C
• rs35239
• ENST00000507733.3:n.313+12202T>G

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.313+12202T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,046 control chromosomes in the GnomAD database, including 51,036 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 0.82 (51036 hom., cov: 31)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 5 publications found

Genes affected

ENSG00000248884 (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 = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.440+95457T>G		intron_variant	Intron 2 of 4
LOC105379013	XR_007058805.1	n.110+26337T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248884	ENST00000507733.3	n.313+12202T>G		intron_variant	Intron 2 of 5	2
ENSG00000248884	ENST00000688207.1	n.65+26337T>G		intron_variant	Intron 1 of 2
ENSG00000248884	ENST00000717704.1	n.110+26337T>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124353 AN: 151928 Hom.: 51002 Cov.: 31

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.818 AC: 124440 AN: 152046 Hom.: 51036 Cov.: 31 AF XY: 0.820 AC XY: 60959 AN XY: 74326

African (AFR) AF: 0.865 AC: 35874 AN: 41476

American (AMR) AF: 0.840 AC: 12835 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2773 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3858 AN: 5162

South Asian (SAS) AF: 0.803 AC: 3869 AN: 4820

European-Finnish (FIN) AF: 0.814 AC: 8614 AN: 10586

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53975 AN: 67936

Other (OTH) AF: 0.810 AC: 1709 AN: 2110

Alfa AF: 0.807 Hom.: 82581

Bravo AF: 0.824

Asia WGS AF: 0.757 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.54
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs35239; hg19: chr5-68029078;