11-78139757-G-T

Position:

• chr11-78139757-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000701360.1(KCTD21-AS1):​n.2G>T 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 0.183 in 691,770 control chromosomes in the GnomAD database, including 13,445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.22 (4384 hom., cov: 34)
  • Exomes 𝑓: 0.17 (9061 hom.)
• Consequence: KCTD21-AS1 ENST00000701360.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.15

Genes affected

KCTD21-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 11-78139757-G-T is Benign according to our data. Variant chr11-78139757-G-T is described in ClinVar as [Benign]. Clinvar id is 1237892.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78139757G>T		intergenic_region
KCTD21-AS1	NR_102280.1	n.-36G>T		upstream_gene_variant
KCTD21-AS1	NR_102281.1	n.-36G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD21-AS1	ENST00000701360.1	n.2G>T		non_coding_transcript_exon_variant	1/3
KCTD21-AS1	ENST00000500113.1	n.-46G>T		upstream_gene_variant		2
KCTD21-AS1	ENST00000523626.6	n.-36G>T		upstream_gene_variant		4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32871 AN: 152062 Hom.: 4377 Cov.: 34

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0965

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.173 AC: 93470 AN: 539590 Hom.: 9061 Cov.: 6 AF XY: 0.174 AC XY: 49834 AN XY: 285958

Gnomad4 AFR exome AF: 0.377

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.289

Gnomad4 SAS exome AF: 0.216

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.216 AC: 32897 AN: 152180 Hom.: 4384 Cov.: 34 AF XY: 0.211 AC XY: 15735 AN XY: 74402

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.0965

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.196

Alfa AF: 0.0526 Hom.: 55

Bravo AF: 0.226

Asia WGS AF: 0.221 AC: 770 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs615116; hg19: chr11-77850803;