22-19323289-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000287146 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664918.1. 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
	ENSG00000287146	ENST00000664918.1		n.363-5109C>T		intron	N/A

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

African (AFR) AF: 0.222 AC: 9197 AN: 41462

American (AMR) AF: 0.300 AC: 4577 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2217 AN: 5174

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4824

European-Finnish (FIN) AF: 0.411 AC: 4341 AN: 10552

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24659 AN: 67934

Other (OTH) AF: 0.304 AC: 643 AN: 2114

Alfa AF: 0.348 Hom.: 37894

Bravo AF: 0.310

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.9
DANN	Benign	0.89
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs982520;

hg19: chr22-19310812;