rs9956150

Positions:

• chr18-32899226-G-A

Variant summary

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

The ENST00000580366.1(ENSG00000263765):​n.28-13607G>A 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 0.853 in 152,214 control chromosomes in the GnomAD database, including 58,715 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 0.85 (58715 hom., cov: 32)
• Consequence: ENST00000580366.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372058	XR_001753390.2	n.1239-1279G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000580366.1	n.28-13607G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129855 AN: 152096 Hom.: 58716 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.853 AC: 129894 AN: 152214 Hom.: 58715 Cov.: 32 AF XY: 0.857 AC XY: 63803 AN XY: 74438

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.994

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.992

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.891

Alfa AF: 0.909 Hom.: 8078

Bravo AF: 0.835

Asia WGS AF: 0.958 AC: 3328 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.93
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9956150; hg19: chr18-30479190;