12-121104028-C-T

Position:

• chr12-121104028-C-T

Variant summary

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

The XR_945458.2(LOC105370031):​n.1622+886G>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 0.109 in 152,184 control chromosomes in the GnomAD database, including 1,591 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 0.11 (1591 hom., cov: 34)
• Consequence: LOC105370031 XR_945458.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

Genes affected

LOC105370031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370031	XR_945458.2	n.1622+886G>A		intron_variant, non_coding_transcript_variant
LOC105370031	XR_945457.2	n.2427+886G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16531 AN: 152066 Hom.: 1586 Cov.: 34

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.109 AC: 16557 AN: 152184 Hom.: 1591 Cov.: 34 AF XY: 0.110 AC XY: 8206 AN XY: 74416

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0468

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.0434

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0505 Hom.: 734

Bravo AF: 0.110

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7298521; hg19: chr12-121541831;