17-50631711-T-C

Position:

• chr17-50631711-T-C

Variant summary

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

The ENST00000502435.1(ENSG00000251239):​n.201+29A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,302 control chromosomes in the GnomAD database, including 47,885 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 0.79 (47848 hom., cov: 33)
  • Exomes 𝑓: 0.72 (37 hom.)
• Consequence: ENSG00000251239 ENST00000502435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

ENSG00000251239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927253	XR_243718.2	n.201+29A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251239	ENST00000502435.1	n.201+29A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119466 AN: 152046 Hom.: 47791 Cov.: 33

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.758

GnomAD4 exome AF: 0.725 AC: 100 AN: 138 Hom.: 37 Cov.: 0 AF XY: 0.730 AC XY: 73 AN XY: 100

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.740

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.786 AC: 119584 AN: 152164 Hom.: 47848 Cov.: 33 AF XY: 0.792 AC XY: 58935 AN XY: 74384

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.761

Alfa AF: 0.751 Hom.: 10935

Bravo AF: 0.795

Asia WGS AF: 0.936 AC: 3257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	18
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2214566; hg19: chr17-48709072;