rs9956150

Variant names:

• chr18-32899226-G-A
• rs9956150
• ENST00000580366.1:n.28-13607G>A

Variant summary

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

The ENST00000580366.1(ENSG00000263765):​n.28-13607G>A variant causes a intron 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: ENSG00000263765 ENST00000580366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 1 publications found

Genes affected

ENSG00000263765 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105372058	XR_001753389.2	n.1131-1279G>A		intron_variant	Intron 7 of 8
LOC105372058	XR_001753390.2	n.1239-1279G>A		intron_variant	Intron 7 of 10
LOC105372058	XR_001753391.2	n.1130+3804G>A		intron_variant	Intron 7 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263765	ENST00000580366.1	n.28-13607G>A		intron_variant	Intron 1 of 2	3
ENSG00000263765	ENST00000798721.1	n.158+11465G>A		intron_variant	Intron 2 of 4
ENSG00000263765	ENST00000798722.1	n.424-13668G>A		intron_variant	Intron 2 of 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

African (AFR) AF: 0.521 AC: 21595 AN: 41474

American (AMR) AF: 0.935 AC: 14301 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3452 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5153 AN: 5172

South Asian (SAS) AF: 0.992 AC: 4789 AN: 4828

European-Finnish (FIN) AF: 0.970 AC: 10293 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67236 AN: 68032

Other (OTH) AF: 0.891 AC: 1885 AN: 2116

Alfa AF: 0.894 Hom.: 8185

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9956150; hg19: chr18-30479190;