12-48027624-G-T

Position:

• chr12-48027624-G-T

Variant summary

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

The XR_001749115.3(LOC105369750):​n.227-2147G>T 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 0.225 in 152,008 control chromosomes in the GnomAD database, including 3,984 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 0.23 (3984 hom., cov: 32)
• Consequence: LOC105369750 XR_001749115.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

Genes affected

LOC105369750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369750	XR_001749115.3	n.227-2147G>T		intron_variant, non_coding_transcript_variant
LOC105369750	XR_001749116.3	n.168-2147G>T		intron_variant, non_coding_transcript_variant
LOC105369750	XR_944904.3	n.227-2147G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34184 AN: 151890 Hom.: 3977 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.225 AC: 34202 AN: 152008 Hom.: 3984 Cov.: 32 AF XY: 0.219 AC XY: 16298 AN XY: 74304

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.258

Alfa AF: 0.199 Hom.: 1070

Bravo AF: 0.231

Asia WGS AF: 0.191 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	12
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12305182; hg19: chr12-48421407;