rs11098090

Positions:

• chr4-110735252-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.145

Alfa AF: 0.142 Hom.: 1180

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11098090; hg19: chr4-111656408;