11-78164340-A-G

Position:

• chr11-78164340-A-G

Variant summary

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

The ENST00000523626.6(KCTD21-AS1):​n.398-9480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 149,696 control chromosomes in the GnomAD database, including 9,063 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 (9063 hom., cov: 32)
• Consequence: KCTD21-AS1 ENST00000523626.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

Genes affected

KCTD21-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCTD21-AS1	NR_102280.1	n.506-9060A>G		intron_variant
KCTD21-AS1	NR_102281.1	n.398-9480A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD21-AS1	ENST00000523626.6	n.398-9480A>G		intron_variant		4
KCTD21-AS1	ENST00000530261.2	n.504-9060A>G		intron_variant		4
KCTD21-AS1	ENST00000662186.1	n.408-9060A>G		intron_variant
KCTD21-AS1	ENST00000663331.1	n.248-9060A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 48598 AN: 149594 Hom.: 9059 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.325 AC: 48607 AN: 149696 Hom.: 9063 Cov.: 32 AF XY: 0.329 AC XY: 24074 AN XY: 73218

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.341

Alfa AF: 0.377 Hom.: 14729

Bravo AF: 0.318

Asia WGS AF: 0.344 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230669; hg19: chr11-77875386;