chr14-55518294-G-A

Position:

• chr14-55518294-G-A

Variant summary

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

The ENST00000554558.6(KTN1-AS1):​n.388-18801C>T 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 0.578 in 152,092 control chromosomes in the GnomAD database, including 26,080 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 0.58 (26080 hom., cov: 32)
• Consequence: KTN1-AS1 ENST00000554558.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

Genes affected

KTN1-AS1 (HGNC:19842): (KTN1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KTN1-AS1	ENST00000554558.6	n.388-18801C>T		intron_variant, non_coding_transcript_variant		4
KTN1-AS1	ENST00000663990.1	n.377-2677C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87889 AN: 151974 Hom.: 26076 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.578 AC: 87922 AN: 152092 Hom.: 26080 Cov.: 32 AF XY: 0.574 AC XY: 42712 AN XY: 74356

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.590

Alfa AF: 0.626 Hom.: 20514

Bravo AF: 0.567

Asia WGS AF: 0.461 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2341883; hg19: chr14-55985012;