rs9807334

Positions:

• chr18-50997791-G-A

Variant summary

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

The XR_007066371.1(LOC107985152):​n.1408C>T variant causes a non coding transcript exon 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: LOC107985152 XR_007066371.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

LOC107985152 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107985152	XR_007066371.1	n.1408C>T		non_coding_transcript_exon_variant	1/3
LOC107985152	XR_001753449.3	n.1002C>T		non_coding_transcript_exon_variant	1/3
LOC107985152	XR_002958225.2	n.1408C>T		non_coding_transcript_exon_variant	1/4
LOC107985152	XR_007066370.1	n.178-13451C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0379

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0908 Hom.: 815

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs9807334; hg19: chr18-48524161;