rs9891572

Variant names:

• chr17-2525214-C-T
• rs9891572
• ENST00000766425.1:n.60-5843C>T

Variant summary

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

The ENST00000766425.1(ENSG00000299795):​n.60-5843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,054 control chromosomes in the GnomAD database, including 2,419 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 0.18 (2419 hom., cov: 32)
• Consequence: ENSG00000299795 ENST00000766425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 17 publications found

Genes affected

ENSG00000299795 (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 (EAS) allele frequency at 95% confidence interval = 0.329 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
ENSG00000299795	ENST00000766425.1	n.60-5843C>T		intron_variant	Intron 1 of 3
ENSG00000299795	ENST00000766426.1	n.69+13181C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26684 AN: 151936 Hom.: 2417 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.176 AC: 26716 AN: 152054 Hom.: 2419 Cov.: 32 AF XY: 0.177 AC XY: 13148 AN XY: 74310

African (AFR) AF: 0.179 AC: 7435 AN: 41474

American (AMR) AF: 0.207 AC: 3156 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1764 AN: 5158

South Asian (SAS) AF: 0.196 AC: 948 AN: 4826

European-Finnish (FIN) AF: 0.172 AC: 1820 AN: 10576

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10233 AN: 67988

Other (OTH) AF: 0.174 AC: 367 AN: 2112

Alfa AF: 0.163 Hom.: 7108

Bravo AF: 0.179

Asia WGS AF: 0.287 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.77
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs9891572; hg19: chr17-2428508;