rs9807334

Variant names:

• chr18-50997791-G-A
• rs9807334
• ENST00000590722.2:n.157+23230G>A

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.157+23230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0644 in 152,250 control chromosomes in the GnomAD database, including 499 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 0.064 (499 hom., cov: 32)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 7 publications found

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985152	XR_001753449.3	n.1002C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC107985152	XR_002958225.2	n.1408C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC107985152	XR_007066371.1	n.1408C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC107985152	XR_007066370.1	n.178-13451C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267699	ENST00000590722.2	n.157+23230G>A		intron_variant	Intron 2 of 8	2		ENSP00000465737.1

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9802 AN: 152132 Hom.: 499 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0644 AC: 9804 AN: 152250 Hom.: 499 Cov.: 32 AF XY: 0.0611 AC XY: 4552 AN XY: 74440

African (AFR) AF: 0.0181 AC: 753 AN: 41552

American (AMR) AF: 0.0379 AC: 580 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4828

European-Finnish (FIN) AF: 0.0888 AC: 941 AN: 10596

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7149 AN: 68010

Other (OTH) AF: 0.0421 AC: 89 AN: 2114

Alfa AF: 0.0859 Hom.: 1291

Bravo AF: 0.0570

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.46
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9807334; hg19: chr18-48524161;