rs9322849

Positions:

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

Variant summary

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

The ENST00000508469.2(ENSG00000248975):​n.70-16052G>T variant causes a intron, non coding transcript 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: ENST00000508469.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000508469.2	n.70-16052G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000549360.1	n.84+75142G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0504

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0462 Hom.: 172

Bravo AF: 0.0711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9322849; hg19: chr14-30690998;