rs1265507

Positions:

• chr12-114430333-A-G
• chr12-114430333-A-T

Variant summary

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

The XR_007063469.1(LOC105369998):​n.86-5256T>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 0.514 in 151,874 control chromosomes in the GnomAD database, including 20,595 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 0.51 (20595 hom., cov: 31)
• Consequence: LOC105369998 XR_007063469.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

LOC105369998 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369998	XR_007063469.1	n.86-5256T>C		intron_variant, non_coding_transcript_variant
LOC105369998	XR_945376.3	n.86-5256T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78067 AN: 151756 Hom.: 20581 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.514 AC: 78123 AN: 151874 Hom.: 20595 Cov.: 31 AF XY: 0.505 AC XY: 37459 AN XY: 74206

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.505

Alfa AF: 0.513 Hom.: 22849

Bravo AF: 0.519

Asia WGS AF: 0.333 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1265507; hg19: chr12-114868138;