ENST00000422599.1:n.1173G>T

Variant names:

• chr20-49957917-G-T
• rs6067284
• ENST00000422599.1:n.1173G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000422599.1(KRT18P4):​n.1173G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 753,176 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0000050 (0 hom.)
• Consequence: KRT18P4 ENST00000422599.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 5 publications found

Genes affected

KRT18P4 (HGNC:16604): (keratin 18 pseudogene 4)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT18P4		n.49957917G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRT18P4	ENST00000422599.1	n.1173G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0000264 AC: 4 AN: 151792 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000725

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000657

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000499 AC: 3 AN: 601384 Hom.: 0 Cov.: 5 AF XY: 0.00000306 AC XY: 1 AN XY: 327292

African (AFR) AF: 0.000114 AC: 2 AN: 17562

American (AMR) AF: 0.0000247 AC: 1 AN: 40452

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20584

East Asian (EAS) AF: 0.00 AC: 0 AN: 35440

South Asian (SAS) AF: 0.00 AC: 0 AN: 67632

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35952

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2510

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 349018

Other (OTH) AF: 0.00 AC: 0 AN: 32234

GnomAD4 genome AF: 0.0000264 AC: 4 AN: 151792 Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2 AN XY: 74082

African (AFR) AF: 0.0000725 AC: 3 AN: 41364

American (AMR) AF: 0.0000657 AC: 1 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67932

Other (OTH) AF: 0.00 AC: 0 AN: 2080

Alfa AF: 0.00 Hom.: 813

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.8
DANN	Benign	0.93
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6067284; hg19: chr20-48574454;