17-27806151-C-T

Variant names:

• chr17-27806151-C-T
• rs34913965
• ENST00000582441.1:c.220-1810G>A

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-1810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,078 control chromosomes in the GnomAD database, including 5,306 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 0.25 (5306 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 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.220-1810G>A		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37560 AN: 151960 Hom.: 5301 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.247 AC: 37586 AN: 152078 Hom.: 5306 Cov.: 32 AF XY: 0.253 AC XY: 18816 AN XY: 74318

African (AFR) AF: 0.108 AC: 4498 AN: 41500

American (AMR) AF: 0.342 AC: 5223 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1499 AN: 5146

South Asian (SAS) AF: 0.352 AC: 1698 AN: 4824

European-Finnish (FIN) AF: 0.322 AC: 3404 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19469 AN: 67970

Other (OTH) AF: 0.237 AC: 502 AN: 2114

Alfa AF: 0.265 Hom.: 9589

Bravo AF: 0.242

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.37
PhyloP100		-0.10

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: rs34913965; hg19: chr17-26133177;