ENST00000656217.1:n.133-15768A>G

Variant names:

• chr10-111804872-T-C
• rs958249
• ENST00000656217.1:n.133-15768A>G

Variant summary

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

The ENST00000656217.1(ENSG00000287231):​n.133-15768A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,024 control chromosomes in the GnomAD database, including 23,601 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 0.54 (23601 hom., cov: 32)
• Consequence: ENSG00000287231 ENST00000656217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

ENSG00000287231 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 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
ENSG00000287231	ENST00000656217.1	n.133-15768A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81970 AN: 151904 Hom.: 23551 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.540 AC: 82085 AN: 152024 Hom.: 23601 Cov.: 32 AF XY: 0.535 AC XY: 39728 AN XY: 74286

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.513

Alfa AF: 0.474 Hom.: 17846

Bravo AF: 0.560

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs958249; hg19: chr10-113564630;