12-12576382-G-A

Position:

• chr12-12576382-G-A

Variant summary

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

The XR_001749010.1(LOC107984486):​n.659-44C>T 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 0.186 in 152,010 control chromosomes in the GnomAD database, including 3,252 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 0.19 (3252 hom., cov: 31)
• Consequence: LOC107984486 XR_001749010.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

LOC107984486 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984486	XR_001749010.1	n.659-44C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28216 AN: 151894 Hom.: 3248 Cov.: 31

Gnomad AFR AF: 0.0746

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.186 AC: 28228 AN: 152010 Hom.: 3252 Cov.: 31 AF XY: 0.180 AC XY: 13381 AN XY: 74254

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.00600

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.203

Alfa AF: 0.220 Hom.: 1653

Bravo AF: 0.186

Asia WGS AF: 0.0700 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12302103; hg19: chr12-12729316;