12-28123693-T-C

Position:

• chr12-28123693-T-C

Variant summary

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

The XR_931461.3(LOC105369710):​n.102+5780A>G 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 0.279 in 151,946 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: LOC105369710 XR_931461.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

LOC107984462 (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 (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984462	XR_001749450.2	n.76+617T>C		intron_variant, non_coding_transcript_variant
LOC105369710	XR_931461.3	n.102+5780A>G		intron_variant, non_coding_transcript_variant
LOC105369710	XR_931462.3	n.102+5780A>G		intron_variant, non_coding_transcript_variant
LOC105369710	XR_931463.2	n.102+5780A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42385 AN: 151828 Hom.: 6100 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.279 AC: 42457 AN: 151946 Hom.: 6124 Cov.: 32 AF XY: 0.273 AC XY: 20290 AN XY: 74284

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.277

Alfa AF: 0.294 Hom.: 10317

Bravo AF: 0.274

Asia WGS AF: 0.138 AC: 485 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.044
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10843104; hg19: chr12-28276626;