rs1188069

Variant names:

• chr14-55503238-T-G
• rs1188069
• ENST00000554558.6:n.388-3745A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000554558.6(KTN1-AS1):​n.388-3745A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,074 control chromosomes in the GnomAD database, including 5,515 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 0.26 (5515 hom., cov: 32)
• Consequence: KTN1-AS1 ENST00000554558.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 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.388-3745A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40188 AN: 151956 Hom.: 5505 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.265 AC: 40235 AN: 152074 Hom.: 5515 Cov.: 32 AF XY: 0.269 AC XY: 20029 AN XY: 74322

African (AFR) AF: 0.309 AC: 12836 AN: 41476

American (AMR) AF: 0.307 AC: 4686 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1274 AN: 5162

South Asian (SAS) AF: 0.354 AC: 1708 AN: 4828

European-Finnish (FIN) AF: 0.297 AC: 3142 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14966 AN: 67974

Other (OTH) AF: 0.261 AC: 551 AN: 2112

Alfa AF: 0.240 Hom.: 5260

Bravo AF: 0.269

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	17
DANN	Benign	0.91
PhyloP100		2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1188069;

hg19: chr14-55969956;