17-27876093-C-T

Variant names:

• chr17-27876093-C-T
• rs4796190
• ENST00000582441.1:c.219+4181G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000266202 (HGNC:):

ENSG00000266527 (HGNC:58314):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266202	ENST00000582441.1	c.219+4181G>A		intron_variant	Intron 3 of 4	4		ENSP00000462879.1
ENSG00000266527	ENST00000581901.1	n.135+1314C>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.914 AC: 37947 AN: 41516

American (AMR) AF: 0.763 AC: 11663 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2418 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2655 AN: 5150

South Asian (SAS) AF: 0.787 AC: 3780 AN: 4802

European-Finnish (FIN) AF: 0.707 AC: 7482 AN: 10576

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43735 AN: 67944

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.672 Hom.: 59766

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
PhyloP100		-1.8

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

Other links and lift over

dbSNP: rs4796190; hg19: chr17-26203119;