rs11098090

Variant names:

• chr4-110735252-T-C
• rs11098090

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 0.145 in 152,184 control chromosomes in the GnomAD database, including 1,881 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 0.14 (1881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22002 AN: 152066 Hom.: 1884 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.145 AC: 21998 AN: 152184 Hom.: 1881 Cov.: 32 AF XY: 0.151 AC XY: 11261 AN XY: 74400

African (AFR) AF: 0.0700 AC: 2907 AN: 41552

American (AMR) AF: 0.235 AC: 3594 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5152

South Asian (SAS) AF: 0.195 AC: 943 AN: 4824

European-Finnish (FIN) AF: 0.205 AC: 2166 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9823 AN: 67996

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.143 Hom.: 4424

Bravo AF: 0.144

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.0
DANN	Benign	0.74
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs11098090; hg19: chr4-111656408;