rs2341883

Variant names:

• chr14-55518294-G-A
• rs2341883
• ENST00000554558.6:n.388-18801C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-55518294-G-A
• chr14-55518294-G-C
• chr14-55518294-G-T

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KTN1-AS1	ENST00000554558.6	n.388-18801C>T		intron_variant	Intron 3 of 3	4
KTN1-AS1	ENST00000663990.1	n.377-2677C>T		intron_variant	Intron 3 of 3

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;