rs579711

Variant names:

• chr11-78145131-C-T
• rs579711
• ENST00000523626.6:n.281-3846C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523626.6(KCTD21-AS1):​n.281-3846C>T variant causes a intron 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 ENST00000523626.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523626.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD21-AS1	NR_102280.1		n.388+3429C>T		intron	N/A
	KCTD21-AS1	NR_102281.1		n.281-3846C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCTD21-AS1	ENST00000523626.6	TSL:4	n.281-3846C>T		intron	N/A
	KCTD21-AS1	ENST00000530261.2	TSL:4	n.386+3429C>T		intron	N/A
	KCTD21-AS1	ENST00000662186.1		n.407+3429C>T		intron	N/A

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

African (AFR) AF: 0.120 AC: 4970 AN: 41474

American (AMR) AF: 0.0994 AC: 1517 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1376 AN: 5162

South Asian (SAS) AF: 0.216 AC: 1037 AN: 4812

European-Finnish (FIN) AF: 0.0977 AC: 1030 AN: 10546

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10711 AN: 68000

Other (OTH) AF: 0.144 AC: 303 AN: 2102

Alfa AF: 0.155 Hom.: 1107

Bravo AF: 0.143

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		-0.70

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs579711;

hg19: chr11-77856177;