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. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554558.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KTN1-AS1	ENST00000554558.6	TSL:4	n.388-18801C>T		intron	N/A
	KTN1-AS1	ENST00000663990.1		n.377-2677C>T		intron	N/A
	KTN1-AS1	ENST00000743879.1		n.389-621C>T		intron	N/A

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

African (AFR) AF: 0.467 AC: 19352 AN: 41474

American (AMR) AF: 0.573 AC: 8760 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2180 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2235 AN: 5168

South Asian (SAS) AF: 0.513 AC: 2474 AN: 4826

European-Finnish (FIN) AF: 0.600 AC: 6342 AN: 10564

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44468 AN: 67992

Other (OTH) AF: 0.590 AC: 1248 AN: 2114

Alfa AF: 0.629 Hom.: 28397

Bravo AF: 0.567

Asia WGS AF: 0.461 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.28
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2341883; hg19: chr14-55985012;