rs11138019

Variant names:

• chr9-79037748-C-G
• rs11138019

Your query was ambiguous. Multiple possible variants found:

• chr9-79037748-C-G
• chr9-79037748-C-T

Variant summary

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

The variant allele was found at a frequency of 0.2 in 152,136 control chromosomes in the GnomAD database, including 3,471 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 0.20 (3471 hom., cov: 32)
• Consequence: KRT18P24 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 1 publications found

Genes affected

KRT18P24 (HGNC:33393): (keratin 18 pseudogene 24)

ENSG00000298572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KRT18P24		n.79037748C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298572	ENST00000756624.1	n.82-7308C>G		intron_variant	Intron 1 of 3
KRT18P24	ENST00000344739.5	n.-180G>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30403 AN: 152018 Hom.: 3460 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.200 AC: 30441 AN: 152136 Hom.: 3471 Cov.: 32 AF XY: 0.201 AC XY: 14922 AN XY: 74364

African (AFR) AF: 0.285 AC: 11805 AN: 41472

American (AMR) AF: 0.265 AC: 4052 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.175 AC: 908 AN: 5182

South Asian (SAS) AF: 0.227 AC: 1096 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1424 AN: 10592

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10171 AN: 67984

Other (OTH) AF: 0.206 AC: 436 AN: 2116

Alfa AF: 0.0733 Hom.: 87

Bravo AF: 0.212

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.19
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs11138019; hg19: chr9-81652664;