17-27876093-C-T

Position:

• chr17-27876093-C-T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.219+4181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,048 control chromosomes in the GnomAD database, including 42,394 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 0.74 (42394 hom., cov: 31)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

ENSG00000266202 (HGNC:):

ENSG00000266527 (HGNC:58314):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.219+4181G>A		intron_variant		4		ENSP00000462879.1
ENSG00000266527	ENST00000581901.1	n.135+1314C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111863 AN: 151930 Hom.: 42338 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.736 AC: 111982 AN: 152048 Hom.: 42394 Cov.: 31 AF XY: 0.741 AC XY: 55069 AN XY: 74306

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.727

Alfa AF: 0.661 Hom.: 40493

Bravo AF: 0.743

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.34

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796190; hg19: chr17-26203119;