5-33181108-T-C

Variant names:

• chr5-33181108-T-C
• rs10072980
• ENST00000510327.2:n.502+82392A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510327.2(ENSG00000250697):​n.502+82392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 151,612 control chromosomes in the GnomAD database, including 48,732 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 0.80 (48732 hom., cov: 30)
• Consequence: ENSG00000250697 ENST00000510327.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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
ENSG00000250697	ENST00000510327.2	n.502+82392A>G		intron_variant	Intron 2 of 2	3
ENSG00000250697	ENST00000657441.1	n.269+116624A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121114 AN: 151498 Hom.: 48681 Cov.: 30

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.800 AC: 121221 AN: 151612 Hom.: 48732 Cov.: 30 AF XY: 0.798 AC XY: 59106 AN XY: 74082

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.791

Alfa AF: 0.816 Hom.: 6309

Bravo AF: 0.795

Asia WGS AF: 0.792 AC: 2752 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10072980; hg19: chr5-33181214;