chr17-27802970-G-C

Position:

• chr17-27802970-G-C

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+1153C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,472 control chromosomes in the GnomAD database, including 11,710 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 0.39 (11710 hom., cov: 29)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27802970G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.438+1153C>G		intron_variant		4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58510 AN: 151354 Hom.: 11704 Cov.: 29

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.387 AC: 58562 AN: 151472 Hom.: 11710 Cov.: 29 AF XY: 0.381 AC XY: 28202 AN XY: 73950

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.401

Alfa AF: 0.382 Hom.: 1236

Bravo AF: 0.395

Asia WGS AF: 0.224 AC: 779 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.68

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: rs2301369; hg19: chr17-26129996;