rs9322849

Variant names:

• chr14-30221792-C-A
• rs9322849
• ENST00000508469.2:n.70-16052G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-30221792-C-A
• chr14-30221792-C-T

Variant summary

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

The ENST00000508469.2(ENSG00000248975):​n.70-16052G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0694 in 152,188 control chromosomes in the GnomAD database, including 542 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 0.069 (542 hom., cov: 32)
• Consequence: ENSG00000248975 ENST00000508469.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• Publications: 3 publications found

Genes affected

ENSG00000248975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508469.2. 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
	ENSG00000248975	ENST00000508469.2	TSL:1	n.70-16052G>T		intron	N/A
	ENSG00000248975	ENST00000549360.1	TSL:3	n.84+75142G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10554 AN: 152070 Hom.: 539 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0694 AC: 10569 AN: 152188 Hom.: 542 Cov.: 32 AF XY: 0.0655 AC XY: 4874 AN XY: 74388

African (AFR) AF: 0.138 AC: 5712 AN: 41522

American (AMR) AF: 0.0362 AC: 554 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0458 AC: 221 AN: 4822

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0504 AC: 3430 AN: 67996

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0505 Hom.: 298

Bravo AF: 0.0711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.8
DANN	Benign	0.84
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9322849; hg19: chr14-30690998;