12-93996709-G-A

Position:

• chr12-93996709-G-A

Variant summary

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

The XR_001749263.2(LOC105369912):​n.89-305C>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 0.0726 in 152,140 control chromosomes in the GnomAD database, including 660 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 (660 hom., cov: 32)
• Consequence: LOC105369912 XR_001749263.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

LOC105369912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369912	XR_001749263.2	n.89-305C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11034 AN: 152022 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0726 AC: 11050 AN: 152140 Hom.: 660 Cov.: 32 AF XY: 0.0730 AC XY: 5433 AN XY: 74376

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0510 Hom.: 82

Bravo AF: 0.0758

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7134340; hg19: chr12-94390485;