rs6505510

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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+27510G>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

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

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.518

Alfa AF: 0.544 Hom.: 43431

Bravo AF: 0.505

Asia WGS AF: 0.378 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs6505510; hg19: chr17-26179790;