rs1463833

Positions:

• chr12-115378637-A-G
• chr12-115378637-A-T

Variant summary

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

The XR_945389.3(LOC105370003):​n.503-4750T>C 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 0.414 in 151,982 control chromosomes in the GnomAD database, including 13,213 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 0.41 (13213 hom., cov: 33)
• Consequence: LOC105370003 XR_945389.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

LOC105370003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370003	XR_945389.3	n.503-4750T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62818 AN: 151866 Hom.: 13203 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.414 AC: 62865 AN: 151982 Hom.: 13213 Cov.: 33 AF XY: 0.416 AC XY: 30875 AN XY: 74274

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.424

Alfa AF: 0.407 Hom.: 21767

Bravo AF: 0.410

Asia WGS AF: 0.462 AC: 1607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.58
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463833; hg19: chr12-115816442;