ENST00000554558.6:n.388-3745A>C

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.

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.388-3745A>C		intron_variant	Intron 3 of 3	4

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 v4.3

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

Other links and lift over

dbSNP: rs1188069; hg19: chr14-55969956;