chr11-78154915-A-G

Position:

• chr11-78154915-A-G

Variant summary

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

The NR_102280.1(KCTD21-AS1):​n.505+5822A>G 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 0.32 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 NR_102280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

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=-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/exons	MANE	Protein	UniProt
KCTD21-AS1	NR_102280.1	n.505+5822A>G		intron_variant, non_coding_transcript_variant
KCTD21-AS1	NR_102281.1	n.397+5822A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCTD21-AS1	ENST00000662186.1	n.407+13213A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.341

Alfa AF: 0.356 Hom.: 1395

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs637149; hg19: chr11-77865961;