ENST00000510327.2:n.503-98564G>C

Variant names:

• chr5-33121891-C-G
• rs1981968
• ENST00000510327.2:n.503-98564G>C

Variant summary

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

The ENST00000510327.2(ENSG00000250697):​n.503-98564G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,092 control chromosomes in the GnomAD database, including 24,697 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 0.55 (24697 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000510327.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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.503-98564G>C		intron_variant	Intron 2 of 2	3
ENSG00000250697	ENST00000657441.1	n.270-98564G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84270 AN: 151974 Hom.: 24646 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.555 AC: 84381 AN: 152092 Hom.: 24697 Cov.: 32 AF XY: 0.551 AC XY: 40927 AN XY: 74330

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.541

Alfa AF: 0.518 Hom.: 2616

Bravo AF: 0.568

Asia WGS AF: 0.499 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981968; hg19: chr5-33121997;