rs7729440

Variant names:

• chr5-170141868-A-G
• rs7729440
• ENST00000518924.1:n.73T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518924.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT18P41	ENST00000518924.1	TSL:6	n.73T>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.327 AC: 2802 AN: 8562

American (AMR) AF: 0.660 AC: 14672 AN: 22222

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 4507 AN: 7000

East Asian (EAS) AF: 0.451 AC: 6991 AN: 15502

South Asian (SAS) AF: 0.669 AC: 32512 AN: 48612

European-Finnish (FIN) AF: 0.527 AC: 8890 AN: 16880

Middle Eastern (MID) AF: 0.610 AC: 614 AN: 1006

European-Non Finnish (NFE) AF: 0.635 AC: 110232 AN: 173564

Other (OTH) AF: 0.590 AC: 8815 AN: 14952

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

African (AFR) AF: 0.345 AC: 14296 AN: 41464

American (AMR) AF: 0.650 AC: 9921 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2310 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2388 AN: 5138

South Asian (SAS) AF: 0.655 AC: 3159 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5545 AN: 10568

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44716 AN: 67978

Other (OTH) AF: 0.571 AC: 1205 AN: 2112

Alfa AF: 0.631 Hom.: 15863

Bravo AF: 0.552

Asia WGS AF: 0.554 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.35
PhyloP100		0.73

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: rs7729440;

hg19: chr5-169568872;