rs9480154

chr6-150289479-G-A

Variant summary

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

The XR_943109.3(LOC105378054):n.560-5301G>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 0.0817 in 152,108 control chromosomes in the GnomAD database, including 662 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 0.082 (662 hom., cov: 32)
• Consequence: LOC105378054 XR_943109.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

Genes affected

LOC105378054 (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 = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378054	XR_943109.3	n.560-5301G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12434 AN: 151992 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0817 AC: 12428 AN: 152108 Hom.: 662 Cov.: 32 AF XY: 0.0852 AC XY: 6334 AN XY: 74362

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0650

Gnomad4 OTH AF: 0.0984

Alfa AF: 0.0726 Hom.: 612

Bravo AF: 0.0803

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.12
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9480154; hg19: chr6-150610615; COSMIC: COSV69430212;