17-27803092-G-A

Position:

• chr17-27803092-G-A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+1031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 137,084 control chromosomes in the GnomAD database, including 28,333 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 0.64 (28333 hom., cov: 21)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27803092G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.438+1031C>T		intron_variant		4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 88254 AN: 137040 Hom.: 28318 Cov.: 21

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.644 AC: 88290 AN: 137084 Hom.: 28333 Cov.: 21 AF XY: 0.649 AC XY: 42496 AN XY: 65504

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.650

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.31

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: rs2301368; hg19: chr17-26130118;