chr12-127819873-C-T

Position:

• chr12-127819873-C-T

Variant summary

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

The ENST00000541797.1(ENSG00000286662):​n.172+1139G>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 0.158 in 152,198 control chromosomes in the GnomAD database, including 2,408 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 0.16 (2408 hom., cov: 32)
• Consequence: ENST00000541797.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000541797.1	n.172+1139G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24083 AN: 152080 Hom.: 2407 Cov.: 32

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.158 AC: 24082 AN: 152198 Hom.: 2408 Cov.: 32 AF XY: 0.162 AC XY: 12037 AN XY: 74398

Gnomad4 AFR AF: 0.0418

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.144

Alfa AF: 0.191 Hom.: 3380

Bravo AF: 0.151

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11059374; hg19: chr12-128304418;