rs1780159

Positions:

• chr9-15157979-T-C

Variant summary

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

The XR_007061423.1(LOC124902123):​n.236-4928T>C 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 0.0779 in 151,056 control chromosomes in the GnomAD database, including 706 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 0.078 (706 hom., cov: 32)
• Consequence: LOC124902123 XR_007061423.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

LOC124902123 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902123	XR_007061423.1	n.236-4928T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11751 AN: 150938 Hom.: 704 Cov.: 32

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0779 AC: 11762 AN: 151056 Hom.: 706 Cov.: 32 AF XY: 0.0759 AC XY: 5607 AN XY: 73852

Gnomad4 AFR AF: 0.0818

Gnomad4 AMR AF: 0.0482

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.0781

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0724

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0778 Hom.: 680

Bravo AF: 0.0766

Asia WGS AF: 0.0540 AC: 186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.4
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1780159; hg19: chr9-15157977;