rs10521218

Variant names:

• chr17-13395543-A-T
• rs10521218
• ENST00000767988.1:n.204-8354T>A

Variant summary

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

The ENST00000767988.1(ENSG00000300019):​n.204-8354T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,070 control chromosomes in the GnomAD database, including 5,344 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 0.26 (5344 hom., cov: 32)
• Consequence: ENSG00000300019 ENST00000767988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 0 publications found

Genes affected

ENSG00000300019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767988.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300019	ENST00000767988.1		n.204-8354T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39700 AN: 151952 Hom.: 5341 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.261 AC: 39722 AN: 152070 Hom.: 5344 Cov.: 32 AF XY: 0.256 AC XY: 19060 AN XY: 74346

African (AFR) AF: 0.253 AC: 10485 AN: 41480

American (AMR) AF: 0.271 AC: 4145 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1043 AN: 3472

East Asian (EAS) AF: 0.152 AC: 783 AN: 5168

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2079 AN: 10572

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19063 AN: 67974

Other (OTH) AF: 0.307 AC: 647 AN: 2110

Alfa AF: 0.260 Hom.: 635

Bravo AF: 0.272

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.52
PhyloP100		-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10521218; hg19: chr17-13298860; COSMIC: COSV69372397;