rs579711

Positions:

• chr11-78145131-C-T

Variant summary

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

The NR_102280.1(KCTD21-AS1):​n.388+3429C>T 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 0.143 in 152,028 control chromosomes in the GnomAD database, including 1,698 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 0.14 (1698 hom., cov: 32)
• Consequence: KCTD21-AS1 NR_102280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCTD21-AS1	NR_102280.1	n.388+3429C>T		intron_variant, non_coding_transcript_variant
KCTD21-AS1	NR_102281.1	n.281-3846C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCTD21-AS1	ENST00000662186.1	n.407+3429C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21739 AN: 151910 Hom.: 1702 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.143 AC: 21735 AN: 152028 Hom.: 1698 Cov.: 32 AF XY: 0.142 AC XY: 10553 AN XY: 74294

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.0977

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.144

Alfa AF: 0.156 Hom.: 1003

Bravo AF: 0.143

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs579711; hg19: chr11-77856177;