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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756624.1. 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
	ENSG00000298572	ENST00000756624.1		n.82-7308C>G		intron	N/A
	KRT18P24	ENST00000344739.5	TSL:6	n.-180G>C		upstream_gene	N/A

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 v4.9

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;