chr12-5138768-G-A

Position:

• chr12-5138768-G-A

Variant summary

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

The XR_931577.2(LOC105369617):​n.535+16284G>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 0.255 in 152,026 control chromosomes in the GnomAD database, including 5,313 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 0.26 (5313 hom., cov: 33)
• Consequence: LOC105369617 XR_931577.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

LOC105369617 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369617	XR_931577.2	n.535+16284G>A		intron_variant, non_coding_transcript_variant
LOC105369617	XR_001748970.2	n.508+16301G>A		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063177.1	n.482+16301G>A		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063178.1	n.491+16301G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38845 AN: 151908 Hom.: 5321 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0478

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.255 AC: 38830 AN: 152026 Hom.: 5313 Cov.: 33 AF XY: 0.253 AC XY: 18836 AN XY: 74312

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.268

Alfa AF: 0.236 Hom.: 985

Bravo AF: 0.243

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs114306; hg19: chr12-5247934;