rs7042542

Positions:

• chr9-121565769-T-G

Variant summary

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

The XR_001746560.2(LOC107987016):​n.134+1082A>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 0.0559 in 152,104 control chromosomes in the GnomAD database, including 418 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 0.056 (418 hom., cov: 31)
• Consequence: LOC107987016 XR_001746560.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

LOC107987016 (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 (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987016	XR_001746560.2	n.134+1082A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8476 AN: 151986 Hom.: 413 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0918

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0559 AC: 8506 AN: 152104 Hom.: 418 Cov.: 31 AF XY: 0.0557 AC XY: 4139 AN XY: 74360

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0281

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.0917

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0462 Hom.: 28

Bravo AF: 0.0603

Asia WGS AF: 0.0660 AC: 232 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	0.91
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7042542; hg19: chr9-124328048;