12-121105208-C-T

Position:

• chr12-121105208-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.1515-187G>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 0.843 in 152,154 control chromosomes in the GnomAD database, including 54,836 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 0.84 (54836 hom., cov: 32)
• Consequence: LOC105370031 XR_945458.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

LOC105370031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370031	XR_945458.2	n.1515-187G>A		intron_variant, non_coding_transcript_variant
LOC105370031	XR_945457.2	n.2320-187G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128135 AN: 152036 Hom.: 54807 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.843 AC: 128221 AN: 152154 Hom.: 54836 Cov.: 32 AF XY: 0.844 AC XY: 62800 AN XY: 74374

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.895

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.872

Alfa AF: 0.885 Hom.: 34460

Bravo AF: 0.845

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1796415; hg19: chr12-121543011;