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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT18P41		n.170141868A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRT18P41	ENST00000518924.1	n.73T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs7729440; hg19: chr5-169568872;