rs11021203

Positions:

• chr11-95544896-G-C
• chr11-95544896-G-T

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 0.12 in 152,186 control chromosomes in the GnomAD database, including 1,309 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 0.12 (1309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.916

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18251 AN: 152068 Hom.: 1308 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.120 AC: 18262 AN: 152186 Hom.: 1309 Cov.: 32 AF XY: 0.119 AC XY: 8842 AN XY: 74398

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.129

Alfa AF: 0.135 Hom.: 195

Bravo AF: 0.114

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
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: rs11021203; hg19: chr11-95278060;