22-19323289-C-T

Variant names:

• chr22-19323289-C-T
• rs982520
• ENST00000664918.1:n.363-5109C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664918.1(ENSG00000287146):​n.363-5109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,008 control chromosomes in the GnomAD database, including 8,014 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 0.32 (8014 hom., cov: 32)
• Consequence: ENSG00000287146 ENST00000664918.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

ENSG00000287146 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372859	XR_938000.3	n.385-5109C>T		intron_variant	Intron 1 of 4
LOC105372859	XR_938001.3	n.385-5109C>T		intron_variant	Intron 1 of 4
LOC105372859	XR_938002.3	n.385-5109C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287146	ENST00000664918.1	n.363-5109C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48233 AN: 151890 Hom.: 8016 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.317 AC: 48236 AN: 152008 Hom.: 8014 Cov.: 32 AF XY: 0.318 AC XY: 23639 AN XY: 74292

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.304

Alfa AF: 0.351 Hom.: 17349

Bravo AF: 0.310

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.9
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs982520; hg19: chr22-19310812;