12-48027251-A-G

Position:

• chr12-48027251-A-G

Variant summary

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

The XR_001749115.3(LOC105369750):​n.227-2520A>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 0.0805 in 152,232 control chromosomes in the GnomAD database, including 519 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 0.080 (519 hom., cov: 32)
• Consequence: LOC105369750 XR_001749115.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

LOC105369750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369750	XR_001749115.3	n.227-2520A>G		intron_variant, non_coding_transcript_variant
LOC105369750	XR_001749116.3	n.168-2520A>G		intron_variant, non_coding_transcript_variant
LOC105369750	XR_944904.3	n.227-2520A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12242 AN: 152114 Hom.: 519 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00538

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0805 AC: 12248 AN: 152232 Hom.: 519 Cov.: 32 AF XY: 0.0809 AC XY: 6024 AN XY: 74438

Gnomad4 AFR AF: 0.0824

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0662 Hom.: 106

Bravo AF: 0.0755

Asia WGS AF: 0.0380 AC: 134 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17122571; hg19: chr12-48421034;