chr11-93071717-T-C

Position:

• chr11-93071717-T-C

Variant summary

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

The ENST00000624450.1(ENSG00000278892):​n.189T>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 0.329 in 152,084 control chromosomes in the GnomAD database, including 11,440 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 0.33 (11440 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000278892 ENST00000624450.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

ENSG00000278892 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93071717T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000278892	ENST00000624450.1	n.189T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49913 AN: 151966 Hom.: 11402 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.329 AC: 50004 AN: 152082 Hom.: 11440 Cov.: 32 AF XY: 0.327 AC XY: 24285 AN XY: 74344

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.299

Alfa AF: 0.249 Hom.: 2520

Bravo AF: 0.348

Asia WGS AF: 0.397 AC: 1377 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531573; hg19: chr11-92804883;