rs12524120

Positions:

• chr6-1365415-T-A
• chr6-1365415-T-C

Variant summary

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

The variant allele was found at a frequency of 0.0749 in 152,308 control chromosomes in the GnomAD database, including 616 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 0.075 (616 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1365415T>A		intergenic_region
LINC01394	NR_187218.1	n.443+23604A>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11407 AN: 152190 Hom.: 616 Cov.: 33

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0769

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

GnomAD4 genome AF: 0.0749 AC: 11412 AN: 152308 Hom.: 616 Cov.: 33 AF XY: 0.0755 AC XY: 5624 AN XY: 74474

Gnomad4 AFR AF: 0.0183

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0756

Alfa AF: 0.0448 Hom.: 49

Bravo AF: 0.0718

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12524120; hg19: chr6-1365650;