chr17-27852764-C-A

Variant names:

• chr17-27852764-C-A
• rs6505510
• ENST00000582441.1:c.219+27510G>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.219+27510G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,942 control chromosomes in the GnomAD database, including 20,266 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 0.51 (20266 hom., cov: 31)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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.219+27510G>T		intron	N/A	ENSP00000462879.1	J3KTA2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77557 AN: 151826 Hom.: 20257 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.511 AC: 77596 AN: 151942 Hom.: 20266 Cov.: 31 AF XY: 0.505 AC XY: 37527 AN XY: 74260

African (AFR) AF: 0.504 AC: 20868 AN: 41424

American (AMR) AF: 0.449 AC: 6864 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1909 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5166

South Asian (SAS) AF: 0.461 AC: 2217 AN: 4812

European-Finnish (FIN) AF: 0.505 AC: 5327 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37278 AN: 67930

Other (OTH) AF: 0.518 AC: 1092 AN: 2108

Alfa AF: 0.538 Hom.: 67650

Bravo AF: 0.505

Asia WGS AF: 0.378 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.55
PhyloP100		-0.088

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs6505510; hg19: chr17-26179790;