chr11-78155234-C-T

Variant names:

• chr11-78155234-C-T
• rs977977
• ENST00000523626.6:n.397+6141C>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.397+6141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,248 control chromosomes in the GnomAD database, including 3,000 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 0.17 (3000 hom., cov: 32)
• Consequence: KCTD21-AS1 ENST00000523626.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCTD21-AS1	NR_102280.1	n.505+6141C>T		intron_variant	Intron 3 of 3
KCTD21-AS1	NR_102281.1	n.397+6141C>T		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+6141C>T		intron_variant	Intron 2 of 2	4
KCTD21-AS1	ENST00000530261.2	n.503+6141C>T		intron_variant	Intron 3 of 3	4
KCTD21-AS1	ENST00000662186.1	n.407+13532C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25850 AN: 151130 Hom.: 3000 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.171 AC: 25843 AN: 151248 Hom.: 3000 Cov.: 32 AF XY: 0.164 AC XY: 12111 AN XY: 73988

African (AFR) AF: 0.0462 AC: 1882 AN: 40718

American (AMR) AF: 0.162 AC: 2461 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.0833 AC: 402 AN: 4824

European-Finnish (FIN) AF: 0.163 AC: 1717 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17815 AN: 67946

Other (OTH) AF: 0.188 AC: 395 AN: 2102

Alfa AF: 0.147 Hom.: 635

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.69
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs977977; hg19: chr11-77866280;