11-78154890-A-G

Position:

• chr11-78154890-A-G

Variant summary

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

The NR_102280.1(KCTD21-AS1):​n.505+5797A>G 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 0.634 in 152,194 control chromosomes in the GnomAD database, including 31,989 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 0.63 (31989 hom., cov: 34)
• Consequence: KCTD21-AS1 NR_102280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

Genes affected

KCTD21-AS1 (HGNC:48674): (KCTD21 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCTD21-AS1	NR_102280.1	n.505+5797A>G		intron_variant, non_coding_transcript_variant
KCTD21-AS1	NR_102281.1	n.397+5797A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCTD21-AS1	ENST00000662186.1	n.407+13188A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96423 AN: 152076 Hom.: 31947 Cov.: 34

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.634 AC: 96511 AN: 152194 Hom.: 31989 Cov.: 34 AF XY: 0.631 AC XY: 46927 AN XY: 74392

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.610

Alfa AF: 0.556 Hom.: 2596

Bravo AF: 0.655

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977978; hg19: chr11-77865936;