rs11119132

Positions:

• chr1-208819087-C-A
• chr1-208819087-C-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 0.0492 in 152,212 control chromosomes in the GnomAD database, including 286 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 0.049 (286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0729 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: 0.0493 AC: 7494 AN: 152094 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0492 AC: 7494 AN: 152212 Hom.: 286 Cov.: 32 AF XY: 0.0474 AC XY: 3526 AN XY: 74426

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0324 Hom.: 33

Bravo AF: 0.0477

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11119132; hg19: chr1-208992432;