rs7729440

chr5-170141868-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518924.1(KRT18P41):n.73T>C 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 0.596 in 460,326 control chromosomes in the GnomAD database, including 84,718 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 0.55 (24806 hom., cov: 32)
  • Exomes 𝑓: 0.62 (59912 hom.)
• Consequence: KRT18P41 ENST00000518924.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.735

Genes affected

KRT18P41 (HGNC:33411): (keratin 18 pseudogene 41)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KRT18P41	ENST00000518924.1	n.73T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84156 AN: 151908 Hom.: 24799 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.616 AC: 190035 AN: 308300 Hom.: 59912 Cov.: 0 AF XY: 0.622 AC XY: 107717 AN XY: 173220

Gnomad4 AFR exome AF: 0.327

Gnomad4 AMR exome AF: 0.660

Gnomad4 ASJ exome AF: 0.644

Gnomad4 EAS exome AF: 0.451

Gnomad4 SAS exome AF: 0.669

Gnomad4 FIN exome AF: 0.527

Gnomad4 NFE exome AF: 0.635

Gnomad4 OTH exome AF: 0.590

GnomAD4 genome AF: 0.554 AC: 84184 AN: 152026 Hom.: 24806 Cov.: 32 AF XY: 0.552 AC XY: 40988 AN XY: 74304

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.571

Alfa AF: 0.633 Hom.: 14198

Bravo AF: 0.552

Asia WGS AF: 0.554 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.1
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7729440; hg19: chr5-169568872;