11-78139778-C-T

Position:

• chr11-78139778-C-T

Variant summary

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

The ENST00000532831.2(KCTD21-AS1):​n.8C>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 0.416 in 636,956 control chromosomes in the GnomAD database, including 58,541 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.36 (11463 hom., cov: 34)
  • Exomes 𝑓: 0.43 (47078 hom.)
• Consequence: KCTD21-AS1 ENST00000532831.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -6.02

Genes affected

KCTD21-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 11-78139778-C-T is Benign according to our data. Variant chr11-78139778-C-T is described in ClinVar as [Benign]. Clinvar id is 1251655.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78139778C>T		intergenic_region
KCTD21-AS1	NR_102280.1	n.-15C>T		upstream_gene_variant
KCTD21-AS1	NR_102281.1	n.-15C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD21-AS1	ENST00000532831.2	n.8C>T		non_coding_transcript_exon_variant	1/2	2
KCTD21-AS1	ENST00000662186.1	n.5C>T		non_coding_transcript_exon_variant	1/3
KCTD21-AS1	ENST00000701360.1	n.23C>T		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54273 AN: 152116 Hom.: 11453 Cov.: 34

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.374

GnomAD4 exome AF: 0.434 AC: 210380 AN: 484722 Hom.: 47078 Cov.: 5 AF XY: 0.435 AC XY: 111739 AN XY: 256896

Gnomad4 AFR exome AF: 0.119

Gnomad4 AMR exome AF: 0.373

Gnomad4 ASJ exome AF: 0.419

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.419

Gnomad4 FIN exome AF: 0.533

Gnomad4 NFE exome AF: 0.460

Gnomad4 OTH exome AF: 0.418

GnomAD4 genome AF: 0.357 AC: 54281 AN: 152234 Hom.: 11463 Cov.: 34 AF XY: 0.361 AC XY: 26852 AN XY: 74422

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.381

Alfa AF: 0.262 Hom.: 727

Bravo AF: 0.334

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	-0.93
CADD	Benign	0.21
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2156785; hg19: chr11-77850824; COSMIC: COSV55202946;