rs12365876

Positions:

• chr11-4393834-T-C

Variant summary

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

The ENST00000641797.4(ENSG00000291144):​n.52T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,142 control chromosomes in the GnomAD database, including 3,281 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 0.20 (3274 hom., cov: 32)
  • Exomes 𝑓: 0.14 (7 hom.)
• Consequence: ENSG00000291144 ENST00000641797.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650

Genes affected

ENSG00000291144 (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 (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4393834T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291144	ENST00000641797.4	n.52T>C		non_coding_transcript_exon_variant	1/3
ENSG00000291144	ENST00000685350.1	n.32T>C		non_coding_transcript_exon_variant	1/3
ENSG00000291144	ENST00000687315.1	n.60T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30174 AN: 151728 Hom.: 3272 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.139 AC: 41 AN: 296 Hom.: 7 AF XY: 0.144 AC XY: 30 AN XY: 208

Gnomad4 AFR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.0652

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.199 AC: 30182 AN: 151846 Hom.: 3274 Cov.: 32 AF XY: 0.196 AC XY: 14567 AN XY: 74222

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.208

Alfa AF: 0.194 Hom.: 2827

Bravo AF: 0.201

Asia WGS AF: 0.0780 AC: 272 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	6.8
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: rs12365876; hg19: chr11-4415064;