rs9302534

chr16-17954853-T-Cchr16-17954853-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001752093.2(LOC107984893):n.364+12690A>G 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 0.478 in 152,144 control chromosomes in the GnomAD database, including 19,696 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 0.48 (19696 hom., cov: 33)
• Consequence: LOC107984893 XR_001752093.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.55

Genes affected

LOC107984893 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984893	XR_001752093.2	n.364+12690A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000569048.5	n.405+12690A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72635 AN: 152024 Hom.: 19656 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.478 AC: 72719 AN: 152144 Hom.: 19696 Cov.: 33 AF XY: 0.470 AC XY: 34991 AN XY: 74384

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.425

Alfa AF: 0.382 Hom.: 15239

Bravo AF: 0.492

Asia WGS AF: 0.399 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	16
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9302534; hg19: chr16-18048710;