rs12156640

Positions:

• chr9-21306242-G-A

Variant summary

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

The XR_001746634.2(LOC107987053):​n.472-30379G>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 0.0732 in 152,124 control chromosomes in the GnomAD database, including 498 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 0.073 (498 hom., cov: 32)
• Consequence: LOC107987053 XR_001746634.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.62

Genes affected

LOC107987053 (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 (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987053	XR_001746634.2	n.472-30379G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11121 AN: 152006 Hom.: 498 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0852

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0732 AC: 11131 AN: 152124 Hom.: 498 Cov.: 32 AF XY: 0.0742 AC XY: 5521 AN XY: 74372

Gnomad4 AFR AF: 0.0316

Gnomad4 AMR AF: 0.0660

Gnomad4 ASJ AF: 0.0852

Gnomad4 EAS AF: 0.0444

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0723

Gnomad4 NFE AF: 0.0923

Gnomad4 OTH AF: 0.0751

Alfa AF: 0.0900 Hom.: 892

Bravo AF: 0.0674

Asia WGS AF: 0.111 AC: 386 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	0.31
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12156640; hg19: chr9-21306241;