chr20-49957917-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422599.1(KRT18P4):​n.1173G>A 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 0.413 in 752,374 control chromosomes in the GnomAD database, including 68,862 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 0.35 (11035 hom., cov: 30)
  • Exomes 𝑓: 0.43 (57827 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53097 AN: 151680 Hom.: 11019 Cov.: 30

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.429 AC: 257729 AN: 600576 Hom.: 57827 Cov.: 5 AF XY: 0.437 AC XY: 142718 AN XY: 326852

African (AFR) AF: 0.124 AC: 2174 AN: 17546

American (AMR) AF: 0.490 AC: 19774 AN: 40374

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 6468 AN: 20572

East Asian (EAS) AF: 0.340 AC: 12019 AN: 35394

South Asian (SAS) AF: 0.561 AC: 37903 AN: 67590

European-Finnish (FIN) AF: 0.558 AC: 20054 AN: 35922

Middle Eastern (MID) AF: 0.319 AC: 800 AN: 2510

European-Non Finnish (NFE) AF: 0.418 AC: 145712 AN: 348472

Other (OTH) AF: 0.398 AC: 12825 AN: 32196

GnomAD4 genome AF: 0.350 AC: 53147 AN: 151798 Hom.: 11035 Cov.: 30 AF XY: 0.364 AC XY: 26977 AN XY: 74134

African (AFR) AF: 0.126 AC: 5205 AN: 41456

American (AMR) AF: 0.441 AC: 6707 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1766 AN: 5150

South Asian (SAS) AF: 0.558 AC: 2674 AN: 4790

European-Finnish (FIN) AF: 0.563 AC: 5925 AN: 10530

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28600 AN: 67882

Other (OTH) AF: 0.359 AC: 753 AN: 2100

Alfa AF: 0.263 Hom.: 813

Bravo AF: 0.324

Asia WGS AF: 0.459 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.2
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; COSMIC: COSV54869430;