chr17-27807685-C-T

Variant names:

• chr17-27807685-C-T
• rs8073782
• ENST00000582441.1:c.220-3344G>A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-3344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,168 control chromosomes in the GnomAD database, including 5,801 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 (5801 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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.220-3344G>A		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40966 AN: 152050 Hom.: 5797 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.269 AC: 40994 AN: 152168 Hom.: 5801 Cov.: 32 AF XY: 0.275 AC XY: 20418 AN XY: 74382

African (AFR) AF: 0.200 AC: 8288 AN: 41504

American (AMR) AF: 0.355 AC: 5437 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5176

South Asian (SAS) AF: 0.348 AC: 1679 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3322 AN: 10580

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19082 AN: 68010

Other (OTH) AF: 0.261 AC: 551 AN: 2112

Alfa AF: 0.278 Hom.: 1168

Bravo AF: 0.267

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
DANN	Benign	0.56
PhyloP100		-0.93

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: rs8073782; hg19: chr17-26134711;