rs34517613

Variant names:

• chr17-28283226-C-T
• rs34517613
• ENST00000577198.6:n.525-5815G>A

Variant summary

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

The ENST00000577198.6(KRT18P55):​n.525-5815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,188 control chromosomes in the GnomAD database, including 722 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 0.090 (722 hom., cov: 31)
• Consequence: KRT18P55 ENST00000577198.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 14 publications found

Genes affected

KRT18P55 (HGNC:):

KRT18P55 (HGNC:26874): (keratin 18 pseudogene 55)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577198.6. 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
	KRT18P55	NR_028334.1		n.525-5815G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT18P55	ENST00000577198.6	TSL:1	n.525-5815G>A		intron	N/A
	KRT18P55	ENST00000581956.2	TSL:3	n.469-5815G>A		intron	N/A
	KRT18P55	ENST00000764155.1		n.110-5815G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13772 AN: 152070 Hom.: 722 Cov.: 31

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0905 AC: 13771 AN: 152188 Hom.: 722 Cov.: 31 AF XY: 0.0880 AC XY: 6544 AN XY: 74400

African (AFR) AF: 0.0425 AC: 1766 AN: 41528

American (AMR) AF: 0.0816 AC: 1246 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.102 AC: 491 AN: 4826

European-Finnish (FIN) AF: 0.0723 AC: 765 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8521 AN: 68006

Other (OTH) AF: 0.107 AC: 226 AN: 2114

Alfa AF: 0.111 Hom.: 1634

Bravo AF: 0.0895

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.91
DANN	Benign	0.45
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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: rs34517613;

hg19: chr17-26610252;