ENST00000523626.6:n.397+5822A>G

Variant names:

• chr11-78154915-A-G
• rs637149
• ENST00000523626.6:n.397+5822A>G

Variant summary

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

The ENST00000523626.6(KCTD21-AS1):​n.397+5822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,254 control chromosomes in the GnomAD database, including 8,942 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 0.32 (8942 hom., cov: 34)
• Consequence: KCTD21-AS1 ENST00000523626.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 4 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCTD21-AS1	NR_102280.1	n.505+5822A>G		intron_variant	Intron 3 of 3
KCTD21-AS1	NR_102281.1	n.397+5822A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCTD21-AS1	ENST00000523626.6	n.397+5822A>G		intron_variant	Intron 2 of 2	4
KCTD21-AS1	ENST00000530261.2	n.503+5822A>G		intron_variant	Intron 3 of 3	4
KCTD21-AS1	ENST00000662186.1	n.407+13213A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48744 AN: 152136 Hom.: 8937 Cov.: 34

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.320 AC: 48754 AN: 152254 Hom.: 8942 Cov.: 34 AF XY: 0.324 AC XY: 24152 AN XY: 74438

African (AFR) AF: 0.133 AC: 5546 AN: 41570

American (AMR) AF: 0.475 AC: 7262 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2021 AN: 5176

South Asian (SAS) AF: 0.374 AC: 1805 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3840 AN: 10596

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25587 AN: 68014

Other (OTH) AF: 0.341 AC: 720 AN: 2114

Alfa AF: 0.348 Hom.: 1399

Bravo AF: 0.320

Asia WGS AF: 0.351 AC: 1218 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	0.33
DANN	Benign	0.24
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs637149; hg19: chr11-77865961;