chr12-118950113-A-C

Position:

• chr12-118950113-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_945428.4(LOC105370020):​n.290-3249T>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 0.654 in 151,984 control chromosomes in the GnomAD database, including 32,615 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 0.65 (32615 hom., cov: 32)
• Consequence: LOC105370020 XR_945428.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987

Genes affected

LOC105370020 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370020	XR_945428.4	n.290-3249T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99326 AN: 151866 Hom.: 32566 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.654 AC: 99438 AN: 151984 Hom.: 32615 Cov.: 32 AF XY: 0.652 AC XY: 48455 AN XY: 74276

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.692

Alfa AF: 0.656 Hom.: 70375

Bravo AF: 0.662

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1997111; hg19: chr12-119387918;