17-27807081-T-C

Variant names:

• chr17-27807081-T-C
• rs9892226
• ENST00000582441.1:c.220-2740A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000582441.1(ENSG00000266202):​c.220-2740A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,996 control chromosomes in the GnomAD database, including 5,942 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 0.27 (5942 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266202	ENST00000582441.1	TSL:4	c.220-2740A>G		intron	N/A	ENSP00000462879.1	J3KTA2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41627 AN: 151876 Hom.: 5936 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.274 AC: 41662 AN: 151996 Hom.: 5942 Cov.: 32 AF XY: 0.279 AC XY: 20746 AN XY: 74294

African (AFR) AF: 0.212 AC: 8802 AN: 41458

American (AMR) AF: 0.358 AC: 5475 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1442 AN: 5166

South Asian (SAS) AF: 0.350 AC: 1688 AN: 4818

European-Finnish (FIN) AF: 0.313 AC: 3303 AN: 10540

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19107 AN: 67956

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.137 Hom.: 251

Asia WGS AF: 0.334 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9892226;

hg19: chr17-26134107;