chr17-27812592-G-A

Position:

• chr17-27812592-G-A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-8251C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,058 control chromosomes in the GnomAD database, including 24,874 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 (24874 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

Genes affected

ENSG00000266202 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27812592G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.220-8251C>T		intron_variant		4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84233 AN: 151940 Hom.: 24870 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.554 AC: 84267 AN: 152058 Hom.: 24874 Cov.: 32 AF XY: 0.559 AC XY: 41550 AN XY: 74310

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.578

Alfa AF: 0.594 Hom.: 11158

Bravo AF: 0.544

Asia WGS AF: 0.682 AC: 2371 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	0.085
DANN	Benign	0.41

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: rs10853181; hg19: chr17-26139618;